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->''"You'd have to explain gay to him first. Then straight! Then why you were still talking when there's ALL THESE SPACESHIPS!! Then [he'd] be very cross it was ever in doubt, add a gay marriage setting to his screwdriver and accidentally marry a Krynoid. Again."''
-->-- '''Creator/StevenMoffat''' (when asked what the Doctor would think of gay marriage)

(For the interested, you can read a blow-by-blow account (pun unintended) of every suspicious moment from almost the entire series ''and'' spinoffs (though the DW section stops with "The Waters of Mars") [[http://www.nyder.com/stuff/whosqueer.html here.]])

[[folder:The Doctor and the Master]]
Basically the OneTruePairing of the series, second only to Doctor/TARDIS (if only because those two have much more screen time together). ChildhoodFriends and fellow students from their youth on Gallifrey, some unknown reason caused a falling out between them. Though one seeks to explore and the other to conquer, their friendship [[FriendlyEnemy still exists despite their enmity]]. Creator/RussellTDavies, Creator/StevenMoffat and Creator/PaulCornell ''all'' ship it, and their feelings towards and obsession with each other had been the subject of much speculation for forty-three years before they finally started snogging on the show. See also [[FoeYay/DoctorWho the Foe Yay page]].

* In "[[Recap/DoctorWhoS8E1TerrorOfTheAutons Terror of the Autons]]" (the Master's very first appearance), the Master isn't at all surprised that the Doctor survived his first two attempts to kill him, and refers to them as the opening salvos in their "game". This begins a trend apparent all throughout Roger Delgado's tenure, with the Master treating their constant battling as more of a friendly rivalry.
** At the end of the episode, despite all the death and destruction the Doctor says he's "rather looking forward to" their next encounter, showing that the Master isn't the only one to enjoy it.
* The Master caring for the Doctor in "[[Recap/DoctorWhoS8E2TheMindOfEvil The Mind of Evil]]", after the Keller machine nearly kills him, is straight out of a HurtComfortFic. Again this starts a trend in which while he continually tries to kill him, the Master always believes the Doctor will survive and doesn't actually want him gone.
* "[[Recap/DoctorWhoS8E4ColonyInSpace Colony in Space]]" has the Master offer the Doctor [[WeCanRuleTogether the opportunity to rule the entire cosmos]]... for seemingly no reason whatsoever, as he doesn't need the Doctor's help. After the Doctor (predictably) refuses, the Master becomes unreasonably angry, implying that he genuinely wanted the Doctor to rule side by side with him.
* "[[Recap/DoctorWhoS9E3TheSeaDevils The Sea Devils]]" has the Master admit that the only reason he keeps trying to destroy Earth is because it's the Doctor's favourite planet. This is part of yet another larger trend in which the Master deliberately targets Earth to infuriate the Doctor, much like a young boy pulling the hair of a girl they like because they don't know how else to express what they're feeling.
* In "[[Recap/DoctorWho20thASTheFiveDoctors The Five Doctors]]", the Master openly states that "a cosmos without the Doctor scarcely bears thinking about", further supporting the idea that he never truly intends to kill the Doctor. He's genuinely nice to the Doctor throughout the entire episode, though the Doctor sadly doesn't believe him, and is very miffed when One doesn't recognise him from their Academy days (what with him having a new, stolen body).
** In that same episode, the Third Doctor calls the Master "my best enemy".
* "[[Recap/DoctorWhoS20E6TheKingsDemons The King's Demons]]" is swimming in HoYay, starting with a very suggestive sword fight between Five and Ainley, and culminating in the Master's revelation that he has a robot that he can transform into the Doctor by sheer force of will. Rather than be weirded out, the Doctor uses his own psychic energy to transform said robot to look like the Master. They spend a few minutes simply playing with their new toy, turning it into each other while giving each other long closeup looks.
** The novelization gives us this absolute gem:
--> The Master moaned in undiluted pleasure. "Only you, dear Doctor, can appreciate my art to the full."
* On two separate occasions ("[[Recap/DoctorWhoS18E6TheKeeperOfTraken The Keeper of Traken]]" and [[Recap/DoctorWhoTVMTheTVMovie the TV movie]]), the Master tries to [[GrandTheftMe steal the Doctor's body]]; he literally wants to be inside the Doctor. The former plays this very sexually, with the Master at one point toying with the ends of the Doctor's long curly hair, while the latter has the line "This body will soon decay. I NEED THE DOCTOR'S BODY!"
* In the game "Destiny of the Doctors", the Master locks up the Doctor and you must free his (then-seven) incarnations. But this is not done without a lot of Anthony Ainley's flirting with him.
* "[[Recap/DoctorWhoS29E12TheSoundOfDrums The Sound of Drums]]" couldn't have stretched the subtext thinner, with a phone conversation that is, in between explaining how the Master survived the Time War, basically the Doctor trying to persuade the Master to have a long term relationship with him and the Master trying to get the Doctor to have phone sex with him. It's so strong that the Master needs to lampshade it, mockingly asking "Are you asking me out on a ''date''?".
** The (in)famous SayMyName bit, where the Master's reaction to hearing his name is closing his eyes and literally ''sighing with pleasure.''
-->'''Master:''' ''Doctor''.\\
'''Doctor:''' Master.\\
'''Master:''' I like it when you use my name.
** This conversation was preceded by the Master scrambling for his phone (he'd had it in his pocket and on speaker) when he hears the Doctor's voice, holding it to his ear with an expression that looks somewhat like relief. Of course, he gets straight into setting off his next plot, but not before swallowing and quietly asking about Gallifrey.
** The previous episode, "[[Recap/DoctorWhoS29E11Utopia Utopia]]", has a similar exchange ("Use my name." "''Master''.") that wouldn't be out of place in a BDSM session.
* "[[Recap/DoctorWhoS29E13LastOfTheTimeLords Last of the Time Lords]]" couldn't get more obvious if it tried. Particularly, the last ten minutes or so, what with [[spoiler:the Master [[DeathIsCheap 'dying']] [[DiedInYourArmsTonight in the Doctor's arms]]]]. And right before this, the Doctor reveals that the only safe place in the universe to keep the Master is... the TARDIS.
-->'''Doctor:''' The only safe place for him is the TARDIS.\\
'''Master:''' You mean you're just gonna... keep me?\\
'''Doctor:''' If that's what I have to do. It's time to change. Maybe, I've been wandering for too long. Now, I've got someone to care for.
* During a bit of timey-wimey shenanigans, the Doctor's [[TheNthDoctor past self]] asks him:
-->'''Fifth Doctor''': Does [the Master] still have [[BeardOfEvil that rubbish beard]]?
-->'''Tenth Doctor''': No, no beard this time. Well, [[TheBeard a wife]].
* Creator/RussellTDavies, writer of all the Master's appearances in Tenth's era, called them "practically soul mates" in a Magazine/RadioTimes interview.
* "[[Recap/DoctorWhoS30E17E18TheEndOfTime The End of Time]]" part one gives us the chase through the scrapyard, complete with piercing stares and heavy panting, the Master zapping the Doctor with his new electricity powers and the Doctor writhing in pain. And when the Master actually ''hits'' the Doctor, he stops attacking and runs over to make sure he's okay. The two reminisce about them playing in fields on Gallifrey as children, before the Master becomes rather insistent that the Doctor ''must understand him'', taking it so far as to initiate a mindmeld.
** Part two is, between the return of [[spoiler:the Time Lords]] and the Doctor's angst about it and his impending death, almost ''entirely'' filled with Ho Yay goodness. Their back and forth banter while the Doctor is locked in what can only be described as [[BoundAndGagged a bondage chair]], the Master taking the Doctor's favourite species and [[spoiler:turning them into copies of himself]] (showing he's still jealous), the Doctor seriously contemplating whether killing the Master is worth saving everyone (which Wilf [[WhatTheHellHero calls him out on]]), and the Master's final act being [[spoiler:to sacrifice himself to save the Doctor]]. This exchange says it all:
-->'''Master''': ''[shaking his head as his eyes fill with tears]'' Don't know what I'd be without that noise.\\
'''Doctor''': I wonder what I'd be without you.\\
'''Master''': ''[tearfully]'' Yeah.
** When talking about the Doctor and Donna ("He ''loves'' playing with Earth girls!"), the Master is annoyed and bitter.
* The Master, in a new android body, lives with the Doctor on the TARDIS in ''WebAnimation/ScreamOfTheShalka''. Paul Cornell later attended a Doctor/Master slash panel (as an audience member) and was asked about the relationship, and replied "I wouldn't be here if I didn't see it" and that in ''Shalka'', the Doctor and the Master were "doing it". He later elaborated that he hadn't intended to write the story that way, but he adores the interpretation.
** Their answering machine message was meant to imply a close friendship between the Doctor and his previous female companion. This was not even ''remotely'' clear in the finished product, and as such, it ends up sounding like the Doctor was recording while the Master was doing R-rated things to him.
** "[[Recap/DoctorWho2013CSTheTimeOfTheDoctor The Time of the Doctor]]" gives us this lovely exchange (which Paul Cornell was downright giddy about):
--> '''Clara:''' I'm cooking Christmas dinner and I may have accidentally invented a boyfriend.\\
'''Doctor:''' Yeah, I did that once, and there's no easy way to get rid of an android!
* In the AudioPlay/BigFinishDoctorWho WhatIf episode [[spoiler: [[Recap/BigFinishDoctorWhoUnboundE2SympathyForTheDevil "Sympathy For The Devil"]]]], the Doctor and the Master meet in alternate regenerations, and the episode explores what would have happened if they'd never met in the 1970's ([[RunningGag or was it the 80's?]]). The HoYay is ''palpable''. This is also one of the times that the Master was played by an openly gay actor... namely, ''[[spoiler: Creator/MarkGatiss]]''.
** In its direct sequel "The Emporium At The End", part of the Franchise/BerniceSummerfield Big Finish range, Benny straight up asks the Master if he and the Doctor used to be lovers. At this point she doesn't even know that the man she's talking to is the Master -- the HoYay is just ''that'' blatant.
* The Creator/BigFinish episode [[Recap/BigFinishDoctorWho049Master "Master"]] might as well have been called "just over two hours of HoYay".
* The Alex [=MacQueen=] incarnation of the Master, also in Creator/BigFinish, is ''by far'' the campest one of them all -- while still being very, very sinister. His plans for Seven involve merging the both of them into a single being, with Seven's mind as a slave to his own, so they can rule the galaxy together for all of eternity. (He fails, of course.) When he finally meets Eight, he spends a while simply admiring the Doctor's beauty, making appreciative noises and commenting on his hair.
* In ''VideoGame/DoctorWhoLegacy'', the Ninth Doctor's reaction to hearing that the Master is involved is simply "Fantastic!"
* In the Creator/BigFinish Short Trips prose story "Christmas Truce", by Creator/TerranceDicks, the Master sneaks into a UNIT Christmas party using an elaborate disguise, a funny accent and a lot of hypnotism... ''just'' so he can spend some time with the Doctor. Three wearily allows it, and the two of them drink some champagne on the UNIT terrace, gaze at the stars and reminisce about the time on Gallifrey they spent hanging out in Shobogan bars. Afterwards, Jo wonders why the Master even bothered planting a bunch of microphones and explosives and such around UNIT base in the process, since the Doctor would inevitably find them anyway -- and the Doctor comments that the Master just really wanted to share a nice glass of champagne with an old friend, but couldn't let his evil reputation get tarnished.
* In the novel "Harvest Of Time", by Alastair Reynolds, the Doctor and the Master spend an inordinate amount of time not killing each other when they have the chance to, and making up rubbish excuses as to why they're letting each other live. The Doctor also goes out of his way to save the Master's life after the latter gets his skull invaded by a tentacled robo-crab.
** Moreover, said robo-crab skull invasion apparently leaves the Master physically weakened, and the Doctor has a rather gentle and considerate manner toward him as a result, helping him stand and such. And we get this rather emotional bit while the Master is out cold:
-->‘If our positions were reversed,’ the Doctor whispered, ‘what would you do? Smother me? Something worse? Or accept that there’s a part of me in you, a part of you in me?’
* In the AudioPlay/BigFinishDoctorWho AU episode "Exile", the Doctor regenerates as a woman. She notices a guy making eyes at her and ''immediately'' assumes he's the Master.
* In "[[Recap/DoctorWhoS34E11DarkWater Dark Water]]", [[spoiler:the Master (well, [[GenderBender Mistress]])]] finally pushes the Doctor up against a wall and snogs him completely senseless. And, being very fond of little games, she offers a snog to Clara as well. She says her heart belongs to the Doctor, teases that her heart is maintained by the Doctor, and clues him in on her [[spoiler:double heartbeat]] by putting his hand on her chest. In the next episode, "[[Recap/DoctorWhoS34E12DeathInHeaven Death in Heaven]]", she tries to ''give him the army she's just spent centuries making'', offering it to him in a desperate attempt to repair their friendship. When the Doctor realises just how utterly broken she is -- and how much he needs her too, just as a reminder of what he's ''not'' -- he [[spoiler: gets down on his knees to gently kiss her on the lips in return]]. Even though [[spoiler:the Master happens to be female at this point]], the arc retroactively canonises several decades of HoYay.
* One script draft of "The End Of Time" had the following scene which, tragically, didn't make it to the screen:
-->'''The Master:''' Yeah, as much as I like looking at myself, I think you can get out of that dress.
-->'''The Master:''' Is that an invitation?
-->'''The Master:''' Now that would be different. And brilliant. But later!
-->'''The Master:''' [[ScrewYourself I'm a psychological minefield.]]

[[folder:Jack Harkness]]
* The Doctor continually curtailing Jack's attempts to flirt with everyone they meet ([[ExtremeOmnisexual male, female, or indeterminate]]) -- allegedly because otherwise they'd never get anything done. It often sounds more like someone's just jealous.
* In "[[Recap/DoctorWhoS27E11BoomTown Boom Town]]", Jack and Nine start pretty much openly flirting, to the point it seems silly to even list it here, because it's not even subtext, it's just text.
-->'''Mickey:''' ''[to Rose]'' You look fantastic! ''[hugs her]''
-->'''Jack:''' Aww, sweet. Look at these two. How come I never get any of that?
-->'''The Doctor:''' Buy me a drink first.
-->'''Jack:''' Such hard work.
-->'''The Doctor:''' ''(grins)'' But worth it!

[[folder:Eleventh Doctor]]
Eleven absolutely doesn't care about social norms or nudity taboos, has NoSenseOfPersonalSpace, and generally brings to television all the lovely things Eight was only allowed to do in the novels. He's also the first incarnation since Eight to randomly kiss companions when he gets excited, without needing some kind of excuse for it.
* Eleven and Rory have a bit of this going on from the moment they meet, mainly thanks to Eleven's complete disregard for personal space and their FoeYay-filled rivalry caused by Amy. It's hilariously one-sided due to Rory's SingleTargetSexuality.
** There is a [[http://youtu.be/Ix6omvPYXWI cut scene]] from "[[Recap/DoctorWhoS31E8TheHungryEarth The Hungry Earth]]" where Eleven gets distracted wondering where Rory is, before stating almost dreamily that "I like him. A ''lot''." It's adorable and most definitely should have been left in.
** And then in "[[Recap/DoctorWhoS31E9ColdBlood Cold Blood]]" Rory [[spoiler:dies to save Eleven]]. Which is followed by Eleven telling Amy to [[spoiler:remember "funny, gorgeous Rory"]].
** The bit in "[[Recap/DoctorWhoS31E7AmysChoice Amy's Choice]]" where the Dream Lord has just sent the three of them off to sleep in one world, and they wake up on a park bench... and [[SleepCute the Doctor's head has fallen onto Rory's shoulder]]. They both kind of freak, and the {{adorkable}}ness reaches near-fatal levels.
*** Also, at one point the Dream Lord sends the Doctor and Rory back into the alternate reality together, offering to "keep" Amy and let the Doctor have Rory all to himself... for all eternity. Rory and the Doctor then proceed to fall asleep entangled together on the floor of the TARDIS.
** Speaking of Eleven's personal space issues, Rory is definitely the most frequent recipient of Doc's hello face-touches.
** During a scene in "[[Recap/DoctorWhoS32E2DayOfTheMoon Day of the Moon]]" when they've all faked their deaths to get into Area 51 and are taken into the Doctor's prison via bodybags, it's Rory who the Doctor goes for straight away and you can see him [[AnywhereButTheirLips kissing his forehead]] to one side of the screen.
** In "[[Recap/DoctorWhoS32E7AGoodManGoesToWar A Good Man Goes to War]]", when Amy and Rory are finally reunited with Melody, they start crying and making out just as the Doctor walks in. He is hastily trying to excuse himself when Rory points his sword at him and ''demands'' he come back.
** The Doctor grabs Rory's head and kisses him full on the mouth in "[[Recap/DoctorWhoS33E2DinosaursOnASpaceship Dinosaurs on a Spaceship]]". Just because he feels like it. [[GuyOnGuyIsHot Amy doesn't seem to mind.]] (Rory makes a "yuck" face.)
*** As was revealed during the 2013 Gallifrey One convention, the snog wasn't actually in the script. Creator/MattSmith just likes kissing people.
** They previously shared a kiss in the [[ComicBook/DoctorWhoIDW IDW comics]], after the Doctor and Amy [[FreakyFridayFlip accidentally switched bodies]]. Rory [[SingleTargetSexuality doesn't even care]] that Amy has a different body and kisses her to reassure her... until he realises that they've already switched back to normal, and he just accidentally kissed the Doctor. (Amy asks them to do it again. [[YaoiFangirl Slower]].)
** In "[[Recap/DoctorWhoS33E4ThePowerOfThree The Power of Three]]", the Doctor looks ''very'' happily at Rory in his underpants. Rory also kisses the Doctor on the cheek in the episode. Just casually. Eleven makes a very happy "oooh!" sound.
* "[[Recap/DoctorWhoS31E1TheEleventhHour The Eleventh Hour]]" has him borrowing a [[MrFanservice hunky guy]]'s laptop, and later in the episode he refers to him as "Amy's friend... the good-looking one". It helps that Jeff seems perfectly happy to let the Doctor get all in his personal space. In fact, cut dialog from that scene even has Jeff's grandmother asking (of the Doctor) "Jeff, is he your gay friend?" despite protests from Jeff that he isn't gay.
* Eleven and [[Recap/DoctorWhoS31E10VincentAndTheDoctor Vincent van Gogh]]. They become physically close right off the bat, with the Doctor doing a lot of clapping his hand on Vincent's shoulder and such. Then Vincent gets hyped up on coffee and ends up screaming "''[[ItMakesSenseInContext Capture my mystery!]]''" at the Doctor, then awkwardly ''stroking'' his shirt. There are lingering glances, the Doctor comforting Vincent in the depths of his depression, long hugs, and [[OneTrueThreesome Amy, the Doctor, and Vincent]] lying on the grass together stargazing, during which scene Vincent takes both their hands, and holds the Doctor's to his chest. [[SugarWiki/HeartwarmingMoments The Doctor even goes against pretty much ALL the rules of time travel and takes Vincent to see how popular and revered his work is in the future, just to add more good moments]] [[TearJerker to a life that inevitably ends in suicide.]]
** In that same episode, Eleven kept running an appreciative eye over Creator/BillNighy as a museum curator because he likes his bow ties.
* "[[Recap/DoctorWhoS31E11TheLodger The Lodger]]" is pretty much a mass of Ho Yay directed at Craig. Eleven strokes him constantly, displays a complete disregard for his personal space and grabbed him at at least one point (although that was for the purposes of telepathy). The Ho Yay of this episode peaked with Eleven stroking Craig's face when he was poisoned and incapacitated, and tenderly saying "You're important". Not to mention Eleven's lack of hesitation in approaching both Craig and Sophie while wearing only a towel.
** Absolutely off the charts in "[[Recap/DoctorWhoS32E12ClosingTime Closing Time]]"; the Doctor plus Craig plus a baby adds up to make the episode one long, unbroken MistakenForGay sequence, and that's not counting the bit where the Doctor attempts to distract Craig from the approaching [[spoiler:Cybermen]] by declaring his passionate love for him and attempting to kiss him to prove it. Craig's only objection, by the way, is that he is already in a relationship.
* "I danced with everyone at their wedding. The women were all brilliant. The men... were a bit shy."
* He considers the founding fathers of the United States "lovely fellas. Two of them fancied me."
* He's friends with Franz Schubert (who was AmbiguouslyBi), and happily babbles about how "Franz the Hands" likes to tickle him while they play the piano together.
* In "[[Recap/DoctorWho2012CSTheSnowmen The Snowmen]]", Eleven goofs around with a Punch handpuppet and snogs it. It proceeds to hit him in the face, not entirely unlike how his relationships typically pan out.
* [=DragonCon=] 2012 had Creator/SylvesterMcCoy giving the world [[https://www.youtube.com/watch?feature=player_embedded&v=5E1i7Wd6aXI Seven/Eleven handpuppet slash]].
* In "[[Recap/DoctorWhoS33E8ColdWar Cold War]]", Eleven tells Creator/DavidWarner [[Recap/DoctorWhoS31E5FleshAndStone "I could kiss you!"]]. Warner's character isn't all too bothered by the idea, since kissing on the mouth was a common gesture of friendship between men in the Soviet era. Eleven looks mildly confused and decides on "later!".
* Eleven and Professor Brian Cox have some of the most intense HoYay in the series so far, in the special "The Science of Doctor Who".

[[folder:Eighth Doctor and Fitz]]
Where to begin with Fitz Kreiner and the Eighth Doctor from the Literature/EighthDoctorAdventures... Over the course of their fifty-something books together, they become [[BiTheWay Not-So-]][[HeterosexualLifePartners Heterosexual Life Partners]]. [=EDAs=] can be divided up into "Fitz and the Doctor are rather gay for each other" books and "Fitz and the Doctor are ''really'' gay for each other" books. This is all massively confusing for Fitz, who has a ''number'' of issues with suddenly being in love with an alien bloke. A ''few'' examples:
* The Doctor happily kisses Fitz on the mouth, after knowing him, from the Doctor's own perspective, for just a couple of weeks.
* He also "delicately" kisses Fitz on the hand, and after spending much of a book looking up and down for him, the Doctor learns Fitz is alive through a video link and kisses the screen in happiness.
** In the same book, Fitz has managed to both sprain and get a shotgun wound in one of his legs. When the group has to make a fast getaway, the Doctor [[BridalCarry carries Fitz bridal style]] to safety. The author thought it was important for everyone to know how "almost romantic" it was.
* Fitz outright admits, via internal monologue, to wanting to "get laid by" the Doctor. When someone uses mind control to make Fitz love her in another book, Fitz breaks out of it by saying, "I've been engineered to love you, Carmodi. With the Doctor - it's the real thing." At one point, the prospect that they may not be able to use the TARDIS comes up and Fitz wonders if they'll end up settling down together in "that house [the Doctor] had in Kent and grow roses."
* While the Doctor is alone on Earth for 100 years, he's obsessed with a song he can only half-remember. "Do you know, I've had a tune going round and round in my head for more than a hundred years. I don’t have the slightest idea what it is. I want to know." It's revealed to the reader at the very end of the book this song is Fitz's, one he wrote for the Doctor. So the Doctor [[TraumaInducedAmnesia forgot everything about himself, the Time Lords, Gallifrey]], but he remembered a song Fitz wrote for him.
* In yet another book, there is the infamous [[HomoeroticDream naked bum-rubbing dream]], causing Fitz to spend the rest of the story trying not to stare at the Doctor's arse. The plot involves a FreakyFridayFlip. The Doctor, who is TheStoic when it comes to expressing sadness or fear, [[NotSoStoic actually]] [[ManlyTears cries]] when he realizes how terrifying [[CowardlyLion Fitz]]'s life is [[TearsOfRemorse because of him]].
* When the Doctor manages to lose Fitz in ''Interference'', he does some very shady things to get him back, including [[spoiler:talking the clone-of-a-clone-of-a-clone of Fitz, a kid named Kode, into suicide so he can basically reprogram memories of Fitz into Kode's body.]] The fact that he lies about it to his other companion implies the Doctor [[{{Necromantic}} knows how sketchy it was.]]
* In that same book, the original Fitz goes to ''extreme'' measures to be re-united with the Doctor, to the point where [[spoiler: after hundreds of years, he's become so obsessed that finding the Doctor has become his unnatural life's entire purpose]].
* The Doctor, generally ObliviousToLove, actually ''flirts'' with Fitz ("I'll show you my tattoo if you're lucky."). Fitz also seems to be the only companion in the [=EDAs=] whose physical appearance the Doctor really notices, and he compliments Fitz when he's looking uncharacteristically well-groomed.
* After spending an entire book having a massive HeroicBSOD, Fitz pulls himself out of it by explicitly making his new purpose in life looking after the amnesiac Doctor.
* Fitz is said to "dote on the Doctor", makes him three meals a day with little notes when he's locked up in his room mourning, and is the target of serious worry from the Doctor sometimes when they are apart.
* The very last line of ''Parallel 59'', which follows the Doctor being joyfully reunited with Fitz and then watching Fitz be reunited with his GirlOfTheWeek, strongly implies that what the Doctor feels for Fitz is love in some sense.
-->He whistled as he walked, Fitz’s plaintive little melody still in his head. Thinking of loved ones, coming home.
* From ''Frontier Worlds'':
--> ‘Doctor! I’ve never been so glad to see anyone in my entire life. And that includes several naked women.’
* There is much more, to the point no fan would be surprised if one of the [=EDAs=] ended with, "And then the Doctor and Fitz went back to the TARDIS and shagged." To see more examples, check [[http://community.livejournal.com/who_otp/188826.html here]] and [[http://community.livejournal.com/ship_manifesto/157884.html here]].
* And last but not least, [[WhatDoYouMeanItsNotSymbolic their first meeting is rife with meaning]]. Fitz is working in a plant shop, lamenting how his life is being wasted away, when the Doctor shows up and tries to purchase a very symbolic flower.
-->"I'd like to buy this begonia."
-->"This begonia? But it's nearly dead."
-->"I know. I intend to rescue it."
** 27 books later, he still has that begonia. As well as Fitz.

Aside from Eight's fascination with Fitz, he was also the first Doctor to be written as bisexual (or as ''anything''-sexual, really) and gets some more lovely moments in the books:
* Eight and UsefulNotes/AlanTuring -- yes, ''that'' Alan Turing -- have some absolutely intense HoYay in the Literature/EighthDoctorAdventures.
* Also, the Eighth Doctor and Karl from the EDA ''The Year Of Intelligent Tigers''. Quoth author Kate Orman:
--> "... still surprised that fans, on the whole, think Karl was in wuv with the Doctor but the Doctor didn't reciprocate. This is not unreasonable in light of canon, but, oh me oh my, I must be more subtle than I thought." [...] "The Doctor and Karl are at it like rabbits every time the reader isn’t looking. However, the precise nature of their relationship is deliberately left ambiguous, so that the reader can interpret it as A) a passionate but platonic friendship or B) unrequited love on the part of Karl. However, I know the location of all the missing sex scenes." [...] "Well, there's the weight of 40 years of apparently sexless Doctor on their side; plus the relationship is *meant* to be ambiguous, so people can interpret it to their comfort level. What surprises me is so few readers *do* think that Karl and the Doctor have to do some fast buttoning and zipping every time I cut back to them." [...] "I wanted to let readers decide for themselves what was happening between the [[strike:sheets]] pages, as a way of showing that you could do a love story for the Doctor with a bit of subtlety and gentleness."
** And Kate Orman being slightly less subtle:
--> "They blow each other every time the camera's off them."
* In the Creator/BigFinish printed story "The Feast of Seven... Eight (and Nine)" by Vanessa Bishop, from ''Short Trips: A Christmas Treasure'', Eight celebrates Christmas by... grabbing some mistletoe and trying to make out with all his former selves. He succeeds with Five and Three. And dreamily sighs about Puccini having such soft lips. And Seven gets offended by the whole thing and tells Eight that Six is "more that way inclined".

Ace gets suspiciously chummy with a female guest cast member in almost every story. We really have to give special mentions to:
* "[[Recap/DoctorWhoS26E2GhostLight Ghost Light]]", in which she [[{{Bifauxnen}} dresses up in Victorian male evening dress for no apparent reason]], and then has two separate {{Cat Fight}}s with a girl who keeps calling her "My Dear".
* "[[Recap/DoctorWhoS26E4Survival Survival]]", in which the Les Yay between her and the Cheetah Person Karra is so shameless that when the author [[WordOfGay complained]] that her [[http://web.archive.org/web/20090101212107/http://www.btinternet.com/~david.darlington/WORDS/RonaMunroInterview.htm intended lesbian innuendo had been censored]] most viewers wondered what the hell could have been cut out that could possibly have been shown before the {{Watershed}}.
* With Mel in "[[Recap/DoctorWhoS24E4Dragonfire Dragonfire]]". Especially when her first response to Mel falling over and being knocked out is to do what is probably meant to be feeling for a skull fracture, but looks more like stroking her hair. It's more blatant in the novelisation, where Ace and Mel [[spoiler:descend an ice face using mountain climbing gear rather than the pack ladder used in the serial]] and [[DoesThisRemindYouOfAnything this exchange takes place]]:
-->'I've never done this before,' admitted Mel. 'You must have done it lots of times.'\\
‘Well, not lots of times…’\\
Ace was avoiding Mel’s eyes.\\
‘How many times?’ asked Mel suspiciously.\\
‘This’ll be the first.’ Ace looked up guiltily. ‘But I’ve seen them do it on telly, and it’s easy!’\\
Mel looked at Ace. The safety harness Ace was wearing didn’t look quite right. ‘I think you’ve got that harness on upside-down. I think those tight straps are supposed to go between your legs.’\\
Ace looked down, and giggled. ‘It’s a good job I’m not a boy!’ she laughed. Mel smiled - and then she began to laugh as well. This wasn’t going to be a bit like they always showed it on telly!
* With Shou Yuing in "[[Recap/DoctorWhoS26E1Battlefield Battlefield]]". They bond over a shared love of explosives and at one point are huddled inside a chalk circle clutching a sword.
* In "[[{{Recap/DoctorWhoS25E2TheHappinessPatrol}} The Happiness Patrol]]" with the repentant Patrol member Susan Q, who talks to her about being closetedly sad. In the deleted scenes package on the DVD, Susan Q tells Ace "As long as you're looking cute we've got a chance".
* Jean and Phyllis in "[[Recap/DoctorWhoS26E3TheCurseOfFenric The Curse of Fenric]]", who also seem rather determined to get Ace to join them early on, and after [[spoiler:they become [[OurVampiresAreDifferent Haemovores]]]] they tell her, "You should have come into the water with us. Then we'd have been together." This is another case where the novelisation goes a bit... deeper with things. Not only is there implied to be a past relationship between Millington and Judson as mentioned below, but it's pretty clear in the book that Jean and Phyllis were probably a couple as well, even before [[spoiler:their [[LesbianVampire transformation]]]].
** Ace definitely had a thing for Kathleen in "Curse of Fenric". Absolutely no sense of personal space, she's constantly taking time (when they really don't have much to spare) to run off and check on her and the baby... She even refuses to accompany the Doctor into a fight because she wants to stay and take care of them. Keep in mind that this is ''Ace [=McShane=]'', who normally refuses to be left behind, hates "dark buildings", and loves a good fight more than anything, turning down the Doctor's request for help in order to barricade herself into a barracks with a sweet, gorgeous, intelligent recently-widowed army wife. [[SurpriseIncest Who happens to be her grandmother.]] And whom she promptly risks her life for to help her escape to London--sending them ''to her own family'', no less.
* With the [[OurWerewolvesAreDifferent alien girl Mags]] in "[[Recap/DoctorWhoS25E4TheGreatestShowInTheGalaxy The Greatest Show In The Galaxy]]". Ace forms a bond with her almost instantly, and seems to pick up on the abusive nature of the girl's arrangement with her companion/master almost before the Doctor does; while Ace is separated from her for most of the episode, they play off one another beautifully when they're together and are among the only characters that never, at any point, doubt one another's honesty or try to use each other.
* Surprisingly, despite all the examples given above on TV, when it comes to the expanded universe novels, Ace becomes almost aggressively promiscuous but exclusively with men, even though in the books they felt free enough to retroactively bring one longstanding TV character (Mike Yates) out of the closet.

[[folder:Tegan and Nyssa]]
* The TARDIS is infinite, and yet Nyssa and Tegan share a very cozy room and not only never question this arrangement, they seem to be pleased as punch about the whole thing. For context, the only other people who have shared a room in the show's history are [[OfficialCouple canon couples]] Ian and Barbara (confirmed to have finally gotten married in [[Series/TheSarahJaneAdventures the SJA]]) and Amy and Rory.
* Nyssa and Tegan hit it off quite well from the very beginning, with Tegan being the more likely to stand up to pushy individuals and Nyssa acting as the voice of reason. This includes their original meeting, where Tegan goes from visibly upset to happy upon seeing Nyssa, at that point a complete stranger.
* Nyssa's gentle fretting and care for Tegan in "[[Recap/DoctorWhoS20E2Snakedance Snakedance]]" edges a great deal past mere friendly concern.
* Nyssa is deeply upset when the Doctor leaves Tegan behind without warning in "[[Recap/DoctorWhoS19E7TimeFlight Time-Flight]]", insisting they shouldn't have just left her.
* In "[[Recap/DoctorWhoS20E1ArcOfInfinity Arc of Infinity]]" Nyssa's priorities pull a 180 from worrying about the Doctor to wanting to hear every detail about Tegan the moment they hear from her. She's very quick to pull Tegan firmly back onto the team when she turns up again, and nearly throws a fit when the Doctor is about to venture into the Matrix to find [[spoiler:Omega]]'s location from Tegan, on the grounds that she might be killed. The next time she sees the Doctor, she won't even ''look at him'' until he tells her Tegan is all right.
* "[[Recap/DoctorWhoS19E5BlackOrchid Black Orchid]]" has this in spades. Tegan cheerfully demonstrates the Charleston for Nyssa. Tegan can tell [[IdenticalStranger Ann and Nyssa]] apart and is insufferably smug about this. (Context: In a discussion between Ann and Nyssa we learn that the only visible difference is ''a mole on Ann's chest'', which isn't visible even in a relatively low-cut butterfly dress.) Upon the reveal of their twin act:
--> '''Muir:''' I might have known they were up to something. Now no one can tell them apart.\\
'''Tegan:''' I can.\\
'''Muir:''' How?\\
'''Tegan:''' ''[smirk]'' That's a secret.
* "[[Recap/DoctorWhoS20E3MawdrynUndead Mawdryn Undead]]" is basically Nyssa and Tegan being married while trying to keep an eye on a bumbling, overgrown alien schoolboy (and Turlough). When not-actually-the-Doctor tries to order Nyssa to dematerialize without Tegan (again), she only argues for a minute... and then walks defiantly out of the TARDIS. The scene where Tegan goes for help is difficult to read as anything ''but'' a worried couple hovering over their injured kid and not knowing what to do, with Nyssa's fretting as she tells Tegan to be careful and to take the TARDIS communicator. For that matter, Tegan's very real fear when she realizes she just left her best friend alone with a stranger who probably isn't the Doctor, upon which she runs back to the TARDIS. The sheer ''relief'' in her voice when she finds Nyssa safe and waiting for them...
* While the rest is [[{{TearJerker}} agonizingly painful]], "[[Recap/DoctorWhoS20E4Terminus Terminus]]" has its moments.
** Nyssa once again demonstrates her priorities:
-->'''Doctor:''' It'll be good to see the TARDIS again.\\
'''Nyssa:''' And Tegan!
** Despite knowing the Doctor longer and having spent more time with him -- all those adventures while Tegan was on Earth -- Nyssa is able to remain calm and collected while saying goodbye to him, asking him politely not to be upset and to let her leave in good faith, to part as friends. Then she has to say goodbye to Tegan and breaks down ''sobbing'' into her chest.
** Tegan's horrified head-shaking in the background when Nyssa tries to tell her that she's chosen to stay on Terminus, and her desperation when she asks the Doctor not to let Nyssa stay on Terminus to die, and her growing realization that Nyssa's really not coming with them. By the time Nyssa asks them to stop trying to convince her so they can part as friends, loud angry defiant Tegan Jovanka can barely manage to whisper "...Please, Nyssa...?" And of course, their tearful goodbye.
-->'''Tegan:''' She'll die here.\\
'''Nyssa:''' ''[voice breaking]'' Not easily, Tegan. Like you, I'm indestructible.
* In the AudioPlay/{{Big Finish|DoctorWho}} adventure "Cradle of the Snake":
** Within the first seven minutes, Tegan (admittedly Tegan possessed, but still) has Nyssa pinned against the wall ''purring'' about how much they'll enjoy themselves if Nyssa stays. Several times it's mentioned that the influence of the Mara works by forcing people's dark sides and ''subconscious desires'' to the surface.
** Throughout the audio and for no reason whatsoever except for its long stay in Tegan's subconscious, the Mara has a sexually-charged ''obsession'' with Nyssa. It sneers about her purity and calls her "little nun", implying that her rejection of its advances ''actually offended it'', and while possessed not only can none of the Mara's minions take their eyes off Nyssa, but the Mara's influence on her involves her [[EvilIsSexy dressing scantily and in black]].
** Nyssa opens the audio by gently shooing Turlough and the Doctor away so she can take care of Tegan on her own. Tegan--who'd locked herself in their room and had refused to open the door for what appeared to be a long period of cajoling by the Doctor--instantly lets Nyssa in when she's asked. One of the first things Nyssa says is that Tegan's been sleeping badly and having nightmares again, to which Tegan's reply is a tired "Sorry to keep you awake." (Admittedly they ''do'' share a room, but if they slept on opposite sides of the room it's very unlikely that Nyssa would be woken up by Tegan's restless sleep unless she actually woke up screaming, which doesn't appear to be the case, so it's logical to conclude they're sharing a bed.)
** Even while under the influence of the Mara ''after it gives the explicit order that Tegan and Turlough are to be killed on sight'', Nyssa goes out of her way to hide Tegan and keep her out of the way of the other members of the Mara's council, to keep her safe. She even consoles Tegan--sort of--about the fact that the Mara rejected the idea of possessing her again, explaining that some people just aren't born to power, and then makes her a very interesting deal...
-->"But I tell you what. If you work hard, I'll let you be my... ''personal assistant''. Would you like that?" (Yes, that pause ''is'' in the actual audio.)

* Writers Creator/PaulCornell, Gareth Roberts, Creator/RussellTDavies and Creator/StevenMoffat all merrily ship a male Doctor with guys, and have all explicitly stated that the innuendo is very much on purpose. Moffat is of the opinion that the Doctor has been flirty with their male and female companions since ever, and that the Doctor, in fact, can't be bothered with silly human concepts of "gay" and "straight". He's also the guy who invented Captain Jack Harkness, and has casually stated that River Song was probably involved with her ''entire'' archaeology crew.
** When asked if the Doctor was bigamous, Moffat replied that River herself probably got married like 428 times, once for each gender. Someone else then asked a question about whether River had ever travelled with Franchise/BerniceSummerfield, to which Moffat replied "remember those 428 marriages..." It took less than 24 hours for Creator/PaulCornell, who invented Bernice, to state that if there were such a thing as a unified Doctor Who canon this would ''totally'' be canon.
* Leela and Romana seemed to get interestingly chummy with the female guest stars.
** And then Leela and Romana became co-stars in the ''AudioPlay/{{Gallifrey}}'' audio series. Romana takes an entire week out of her schedule as the ''President of Gallifrey'', with no warning, specifically to take Leela to a spa planet and talk about their relationship. They proceed to talk about Romana's regenerations in the context of reassuring Leela that unlike ''her husband'', Romana will never leave her.
-->'''Leela:''' I was so alone in the world of dreams when you left... the wild lands were dark, and so ''quiet''... I... I do not wish to be alone.\\
'''Romana:''' There will be a place for you with me, always. ''Whatever'' face I wear.
** In that same episode, they manage to accidentally get into a jumbled-up [[spoiler:FreakyFridayFlip]], which Romana calls "intoxicating".
** In "[[Recap/DoctorWhoS14E5TheRobotsOfDeath The Robots of Death]]", Toos seems unusually attached to Leela, to the point that she requested Leela check on her arm again even after a robot offered to take her to Sickbay. Toos then proceeds to have a nice elaborate SecurityCling with Leela on her bed, surreptitiously groping her naked thigh.
** Donna picks up where Leela and Romana left off in the "getting chummy with female guest stars" category, namely Evelina in "[[Recap/DoctorWhoS30E2TheFiresOfPompeii The Fires of Pompeii]]", Martha and Rose in their guest appearances, Jenny in "[[Recap/DoctorWhoS30E6TheDoctorsDaughter The Doctor's Daughter]]", and flipping ''Creator/AgathaChristie'' in "The Unicorn and the Wasp". Special mention goes to Miss Evangelista in "Silence in the Library"/"Forest of the Dead", to the point that her [[spoiler:dying request]] is to speak to Donna, and she deliberately seeks Donna out in [[spoiler:CAL's simulated world.]]
* A memorable moment between Creator/WilliamShakespeare and the Tenth Doctor in "[[Recap/DoctorWhoS29E2TheShakespeareCode The Shakespeare Code]]" (keep in mind the real Shakespeare is widely speculated to have been bisexual):
-->'''Doctor''': Come on, we can all have a good flirt later!\\
'''Shakespeare''': Is that a promise, Doctor?\\
'''Doctor''': Oh, [[http://en.wikipedia.org/wiki/Sonnet_57 fifty-seven academics]] just punched the air.
* This exchange in "[[Recap/DoctorWhoS29E4DaleksInManhattan Daleks in Manhattan]]":
-->'''Martha:''' I'm so glad to see you!\\
'''Tenth Doctor:''' Yeah, well you can kiss me later. You too Frank, if you want.
* The Second Doctor and Jamie. [[http://static.tvtropes.org/pmwiki/pub/images/1grope_6685.jpg Getting]] [[http://static.tvtropes.org/pmwiki/pub/images/2grope_7217.jpg all]] [[http://static.tvtropes.org/pmwiki/pub/images/3grope_5587.jpg up]] [[http://static.tvtropes.org/pmwiki/pub/images/4grope_2091.jpg in]] [[http://static.tvtropes.org/pmwiki/pub/images/5grope_9209.jpg each]] [[http://static.tvtropes.org/pmwiki/pub/images/6grope_1475.jpg other's]] [[http://static.tvtropes.org/pmwiki/pub/images/7grope_139.jpg personal]] [[http://static.tvtropes.org/pmwiki/pub/images/8grope_1542.jpg space,]] [[http://static.tvtropes.org/pmwiki/pub/images/9grope_3281.jpg oh]] [[http://static.tvtropes.org/pmwiki/pub/images/10grope_2357.jpg yes.]] They hug constantly, they flirt, they banter like an old married couple, and of all the companion/Doctor relationships, they seem most like a dynamic duo rather than "the extraordinary Doctor and his amazed companion along for the ride". The actors were very close friends, and Frazer Hines commented that he could read Troughton's mind just by looking into "those twinkling eyes", and that much of their thoughts of spending time with each other sadly had to remain "private".
** Not just constant hugging, but constant touching -- they ''epitomize'' NoSenseOfPersonalSpace. Jamie is a master of the SecurityCling and, while he'll grab onto his co-companions or random one-off characters who happen to be nearby, clings to the Doctor with truly ridiculous frequency.
** That moment when the Doctor fondles Jamie's sporran, and a scene which only survives in telesnaps but which depicts [[ManInAKilt Jamie]] on the Doctor's shoulders -- and the Doctor rather definitely looking up.
** In "[[Recap/DoctorWhoS4E9TheEvilOfTheDaleks The Evil of the Daleks]]", when the Doctor has to manipulate Jamie as part of a plot and Jamie finds out, he tells the Doctor "We're finished!" and refuses to touch him. (It doesn't last long.) And the ''sheer terror'' on the Doctor's face when he finds out that the Daleks want to use Jamie in their experiments. Not until the Revival series would a Doctor go into a similar panic at the thought of a companion being harmed.
* Turlough. There certainly seems to be some mutual crushing going on in "[[Recap/DoctorWhoS20E3MawdrynUndead Mawdryn Undead]]", Turlough's first episode; it would also explain the Doctor's otherwise inexplicable decision to trust Turlough ''after Turlough has introduced himself by trying to steal the TARDIS''. There's also this line, from the commentary, on the subject of why the Doctor trusts him so easily:
-->'''Peter Davison:''' Clearly I'm [[AlasPoorScrappy missing Adric]] so much... I clearly want a companion I can [[HoYay put my arm around,]] [[NoHuggingNoKissing rather than one I cannot touch, as with the girls.]]
* Wilf almost has a mancrush on the Doctor.
* Malcolm? Hero-worship is understandable, but running up to the Doctor, hugging him ''very'' tightly, and saying "I love you!" over and over is a ''bit'' different.
* The increasingly HoYay interactions between Max Stael and Adam Colby in "[[Recap/DoctorWhoS15E3ImageOfTheFendahl Image of the Fendahl]]", which escalates to Adam being tied to a column with three buttons of his shirt unbuttoned and Max stroking his face with a pistol. Scott Fredericks has stated he deliberately played Max as bisexual.
* Mr. Finch from "[[Recap/DoctorWhoS28E3SchoolReunion School Reunion]]" softly asking the Doctor to rule the universe at his side to a background of piano music comes to mind.
* In "[[Recap/DoctorWhoS28E5RiseOfTheCybermen Rise of the Cybermen]]" / "[[Recap/DoctorWhoS28E6TheAgeOfSteel The Age of Steel]]" there was [[spoiler:Rickey/Alternate Mickey]] and his boyfriend Jake. The [[http://www.youtube.com/watch?v=i3MzNvT5q6E actual expository scene]] was cut for one reason or another, making their canon relationship into simply oodles of hoyay.
* In "[[Recap/DoctorWhoS31E6TheVampiresOfVenice The Vampires of Venice]]" we get lots of Les Yay from Signora Calvierri, who is basically a dominatrix-y older woman surrounded by sexy younger women who she regularly drinks blood from. (At one point this included Amy.)
* Adric has huge HoYay with both Four AND Five. Lots of longing glances, and thoroughly unnecessary compliments of the Doctor, such as one bit where he says something along the lines of "Oh, Doctor, your handwriting is just lovely", in this really quite suggestive way. Not to mention his persistent daddy issues with just about any powerful male figure the team encounters, evil or not. (Not really relevant, but his actor Creator/MatthewWaterhouse is gay.)
* In the 2011 Comic Relief Red Nose Day mini episode "Time": Amy Pond and [[spoiler:[[ScrewYourself Amy Pond]]]].
-->'''Amy''': Mmm... I'd give you a driving licence.\\
'''[[spoiler:Amy]]''': I'll bet you would.\\
'''The Doctor''': Oh, this is how it all ends. Pond, flirting with [[spoiler:herself]]. True love at last. ''[remembers that Amy's husband is also present]'' Oh, sorry Rory.\\
'''Rory''': ''[nearly catatonic]'' ...[[TwinThreesomeFantasy absolutely no problem at all...]]
* Madame Vastra and her chambermaid Jenny from "[[Recap/DoctorWhoS32E7AGoodManGoesToWar A Good Man Goes To War]]" do not qualify simply because it's definitely not ''sub''text. It's canon as of "The Snowmen", where Vastra introduces Jenny as her wife.
** Also in "[[Recap/DoctorWho2012CSTheSnowmen The Snowmen]]", Vastra is definitely hitting on Clara while "testing" her. Jenny doesn't seem to mind.
** Once again, Vastra and Clara's... [[SecretTestOfCharacter argument...]] in "[[Recap/DoctorWhoS34E1DeepBreath Deep Breath]]" positively reeks of HoYay, and this time Jenny minds a little bit.
-->'''Clara''': Now just because my pretty face has turned your head, do not assume that I am so easily distracted.\\
'''Vastra''': Well. Goodness me. The lake has been ruffled. I often wondered what you'd be like when you lost your temper.\\
'''Jenny''': ''[hits Vastra over the head]'' Oi! Married!\\

* In "[[Recap/DoctorWhoS6E3TheInvasion The Invasion]]", Isobel is quite clear that she only wants to photograph Zoe, not Jamie. And then she gets Zoe to wear a miniskirt, and [[PantyShot photographs her from floor level]].
* There is a definite, if subtle, romantic undertone to Rumford and Fay's relationship in "[[Recap/DoctorWhoS16E3TheStonesOfBlood The Stones of Blood]]". Mary Tamm herself said "We were all so innocent back then" when the LesYay was pointed out to her.
* "[[Recap/DoctorWhoS26E3TheCurseOfFenric The Curse of Fenric]]":
** Two of the only survivors of the serial are a British soldier and a Russian soldier who decide there isn't any point to fighting anymore, and who are last seen with their arms wrapped around each other with big grins on their faces.
** The novelisation outright states that Millington was in love with Judson, and their sourness towards each other is in part because it ended very badly.
** When Jean and Phyllis tell Miss Hardaker that they're going to Maidens' Point (they had agreed to meet Ace there), she gets angry and says, "I know what girls who go to Maidens' Point have in mind!" You expect her to follow this up with something like "You're going there to meet with boys!" But no, boys aren't mentioned ''at all'' in this little lecture; just "girls with evil in their hearts". In the novelisation, by the same author, it's not even subtle:
--> ‘I don’t know why I let you talk me into doing these things. You’re always getting me into trouble.’ ‘’Cause it’s a laugh, that’s why. And anyway, if it weren’t for me, you’d still be a baby doll – know what I mean?’ Jean smiled slyly. Phyllis turned bright red and Jean laughed.
* Why was Ping-Cho in "[[Recap/DoctorWhoS1E4MarcoPolo Marco Polo]]" so anxious for Susan to say "goodbye" to her?
* In "[[Recap/DoctorWhoS29E4DaleksInManhattan Daleks in Manhattan]]", Martha seems way too excited to watch Tallulah's dance number.
* "[[{{Recap/DoctorWhoS25E2TheHappinessPatrol}} The Happiness Patrol]]" is loaded with Ho Yay to the point that there's a serious argument that the whole thing is a deliberate queer rights allegory. As well as Ace's friendship with Susan Q (mentioned above), the dysfunctional relationship between Gilbert M and the Kandyman really is like a married couple turned sour, and of course Gilbert M and Joseph C run away together at the end. In the deleted scenes, Gilbert M's reaction to the Kandyman's death is "There's nothing here for me now.", at which point Joseph C makes a suggestion...
* At the end of "[[Recap/DoctorWhoS8E5TheDaemons The Daemons]]", everyone merrily joins in the DancePartyEnding and the local witch makes sure to point out that it's a ''fertility'' dance. Hearing that, Captain Yates asks the Brigadier: "Fancy a dance, sir?" ("Kind of you Captain... I think I'd rather have a pint.") The "Making of" segment of the DVD has Creator/NicholasCourtney pretty much confirm (as quoted by Creator/KatyManning) what we were already thinking -- "The Brig's an alcoholic and Mike Yates is gay!". According to the ''Literature/DoctorWhoNewAdventures'', Mike eventually ends up with a guy.
** At the beginning of "[[Recap/DoctorWhoS11E5PlanetOfTheSpiders Planet of the Spiders]]", the Doctor takes the Brigadier to see a variety show of which one act is an exotic dancer. The Brigadier enjoys the act, but apparently because he 'will have to adapt some of those exercises for the men'.
* Jex and Isaac from "[[Recap/DoctorWhoS33E3ATownCalledMercy A Town Called Mercy]]": Isaac's [[HeroWorshipper gushing over Jex]], and despite [[TheReveal the twist]] of the episode, his [[spoiler:[[DyingDeclarationOfLove last words]]]] pretty much being "take care of Jex for me". It isn't fully one-sided either: Jex has serious [[SurvivorsGuilt survivor's guilt.]] "He was my...friend."
* The Doctor's friendship with the Corsair has serious Ho Yay overtones. According to Creator/NeilGaiman, (s)he and the Doctor occasionally woke up in cells together after bouts of heavy drinking. (And once in the vault of the Bank of England.)
-->"Fantastic bloke. He had that snake as a tattoo in every regeneration. Didn't feel like himself unless he had that tattoo. Or herself, a couple of times. Oo-hoo! She was a bad girl!"
* Giuliano and Marco in [[Recap/DoctorWhoS14E1TheMasqueOfMandragora "The Masque Of Mandragora"]] are beyond blatant, with UndyingLoyalty on both ends. Giuliano trusts Marco enough to confide in him unquestioningly despite his uncle's spies being everywhere, while Marco is so devoted to the Count he'll willingly endure Medieval-style torture rather than betray him. Marco also says "We have weapons of our own" while staring at Guiliano's crotch.
** Giuliano appears to be attracted to the Doctor in their first scene together, looking him up and down appraisingly and remarking, "a most uncommon spy!". At the end of the story he [[VisualPun literally gives the Doctor a large sausage]].
* In [[Radio/ThirdDoctorRadioDramas "The Ghosts Of N-Space"]], the Doctor fondly recalls how he and his old teacher used to go skinny dipping on Gallifrey. (And earlier in the episode, Sarah Jane -- posing as a page boy -- gets mistaken for the Doctor's ''catamite''.)
* As the Great Intelligence, Creator/RichardEGrant grabs the Doctor's face with a black leather glove and brings their mouths close together while they stare defiantly at each other.
* As ''The Discontinuity Guide'' points out, there's only one bed in [[LoverAndBeloved Izlyr and Ssorg's]] room in "[[Recap/DoctorWhoS9E2TheCurseOfPeladon The Curse of Peladon]]".
* ''Magazine/DoctorWhoMagazine'' comic companions Izzy and Fey share a bit of flirtation, a lot of adventures, and -- once Izzy manages to overcome her fear and be open about her sexuality -- a nice proper snog.
** Izzy and Destrii blatantly flirt with each other when they first meet, with Destrii calling her new friend "Sweetie" and commenting on her body a lot, and Izzy just making cute faces and happily jumping on Destrii's back at the first opportunity. Too bad [[spoiler:Destrii reveals herself to be evil and ends up taking Izzy's body, but not in ''that'' way]].
** There's a distinct undercurrent of something between Majenta Pryce and her sometime-cellmate Zephyr (with Majenta deciding to take Zephyr along in the TARDIS, which ends up getting nixed by the plot), and the end of Majenta's arc sees the two of them heading off together to seek their fortune. Amusingly, emails between [=RTD=] and the magazine staff included the stipulation "No more lesbians" -- either he wasn't actually serious, or they figured [[ExactWords bi women were still fair game.]]
* The implications of Rose ending up with the clone Doctor in the end of "[[Recap/DoctorWhoS30E12TheStolenEarth The Stolen Earth]]" / "[[Recap/DoctorWhoS30E13JourneysEnd Journey's End]]", and the clone Doctor saying something to her that we didn't hear ends with them kissing. For the Doctor to properly return Rose's love, and say what she needed to hear, he had to be part human. Specifically, part Donna.
** Speaking of which, some of Donna and Rose's interactions in "Turn Left" could be interpreted as Les Yay.
* [[WordOfGay Word Of Moffat]] says Tasha Lem and Madame Kovarian were married, before the whole Trenzalore thing caused the schism in the Church.
* [[Recap/DoctorWhoS34E3RobotOfSherwood "Robot of Sherwood"]] pits the Twelfth Doctor and Robin Hood against each other in a fencing match, wherein the Doctor (armed with a spoon) brags about all the fencing masters he'd fenced with, including Creator/ErrolFlynn, whom he proceeds to remark has a very big [[LastSecondWordSwap "ego"]]. A major GettingCrapPastTheRadar moment, as grown ups would connect the dots and figure what the Doctor [[BiggusDickus meant to say]], leading to the impression that the "fencing" with Flynn was something else entirely. (And although it wasn't in the script, Clara adds a polite little cough.)
* In [[Recap/BigFinishDoctorWho054TheNaturalHistoryOfFear Jim Mortimore]]'s novel ''[[http://doctorwho.org.nz/archive/campaign/ Campaign]]'', which was commissioned by the BBC and then immediately rejected for making ''[[Anime/NeonGenesisEvangelion End Of Evangelion]]'' look normal, the First Doctor's companions are thrust into different times and places. This includes Ian being thrown into the Great Fire of London, where he ''and'' an alternate version of him (Cliff, named for an early version of Ian when ''Doctor Who'' was first pitched) replace a blacksmith and his wife (originally from the novella "Doctor Who and the Invasion from Space"). Cast in these roles, they realise their love is forbidden, but they're hopelessly stuck in a WorldLimitedToThePlot and spend their moments together in the GroundhogDayLoop as a married couple... and stay lovers once they escape. (There's also a brief moment where Alexander the Great refers to a version of Ian as his "beloved", but good luck figuring out where it fits into all the rest of the MindScrew. The original commissioned pitch for the novel made it clear that Alexander had fallen in love with Ian.)
* Speaking of Ian Chesterton, "[[Recap/DoctorWhoS2E8TheChase The Chase]]" gives us a classic moment:
--> '''Ian:''' You've done it again! You've beaten them! \\
'''First Doctor:''' My dear boy, I could kiss you!
* And speaking of Alexander the Great, the AudioPlay/BigFinishDoctorWho story "Farewell, Great Macedon" has some intense HoYay between Alexander and Hephaistion. Historians have yet to determine whether the two men were lovers or just best friends, and the audio deliberately leaves it ambiguous, presenting the word "love" and Hephaistion's (gorgeous) description of how much Alexander means to him as something that can mean either romance or friendship. (Since the audio was adapted from a script that never made it to TV, one can't help but wonder what the original looked like.)
* Clara Oswald has shown romantic feelings for both the Doctor (Eleventh and Twelfth) and Danny Pink, but she also [[AmbiguouslyBi may or may not be attracted to women.]] Oswin, [[ItMakesSenseInContext a copy of Clara along the Doctor's timestream]], flirted with both Rory and Amy, and also casually mentioned a girl called Nina she had a crush on. Clara herself carries on Ace's tradition of getting very chummy with female guest stars; she compares Journey Blue in "Into the Dalek" to her future boyfriend Danny and got very close with Maisie in "Mummy on the Orient Express." There was also that time she asked the Eleventh Doctor to [[TheBeard pretend to be her boyfriend at her family's Christmas dinner.]]
** In "The Magician's Apprentice", she has [[NoodleIncident this line]], which is... less ambiguous.
--> '''Clara:''' ''(teaching a class)'' Jane Austen. Amazing writer, brilliant comic observer, and, strictly among ourselves, a phenomenal kisser.
*** In "[[Recap/DoctorWhoS35E10FaceTheRaven Face the Raven]]", they apparently had enough of a relationship to have Clara say she loves her. "[[LampshadeHanging Take that how you like]]".
** Although she doesn't have much interaction with Ashildr in [[Recap/DoctorWhoS35E5TheGirlWhoDied "The Girl Who Died"]], she does notice the Doctor's interest in Ashildr, and jokes "I'll fight you for her". The needle goes in deeper with the Doctor's odd reply about humans "being obsessed".
** And then, at the end of "[[Recap/DoctorWhoS35E12HellBent Hell Bent]]", we have Ashildr and Clara [[spoiler: flying off to see the universe in a stolen TARDIS]].
** And then there's her subtext with Missy. They both seem to hate each other, but if you look ''really'' closely (or just have ShippingGoggles on) some of their interactions are rather suggestive. Examples include:
*** Missy, while pretending to be a "welcome droid", volunteers to kiss Clara. Seriously. After she gives Twelve the "3W Greeting's Package" and snogs him, she turns to Clara and says "You also have not received the welcome package" and moves to make-out with her too before Clara (unfortunately) declines.
*** Then there's the fact that Missy "conveniently" had a pair of ''handcuffs'' on her to attach to Clara so they could get a Dalek casing and sneak into the city. It's certainly very interesting she actually had handcuffs on her for her adventure with Clara.
*** Then just before they get the Dalek casing, it explodes and Missy shields Clara ''with her body!'' [[http://49.media.tumblr.com/4c8820f80e8567e7c71fa880e5da95d1/tumblr_nvb2igvEPa1r0bnq5o5_250.gif It looks very suggestive.]]
*** Then there's her telling Clara to say "I love you" when she's in the Dalek casing. She even says "Don't ask me why, ''just say it.''" And Clara actually says it!
** Then there's "Clara and the TARDIS," wherein Clara gives [[ScrewYourself herself]]... long story, a lascivious look, and declares that they have to share a bed.
* You can make a serious argument that Nyder in "[[Recap/DoctorWhoS12E4GenesisOfTheDaleks Genesis of the Daleks]]" is Davros's StalkerWithACrush. It's one of the reasons why "Genesis of the Daleks" is one of the serials with a massive LGBTFanbase ''of its own''. In the blog ''Adventures With the Wife in Space'', Neil opines to Sue that Nyder is in love with Davros and she accuses him of 'reading too far into this'.
* [[http://shabogangraffiti.blogspot.co.uk/2012/12/vixens-and-saxons.html This blog post]] makes a reasonably serious argument that Irongron and Linx's disastrous partnership in "[[Recap/DoctorWhoS11E1TheTimeWarrior The Time Warrior]]" is rather like a DestructiveRomance, pointing out how Irongron is fascinated by Linx's face, Linx cuts Irongron off from all his other friends, that Irongron has several scenes moaning to his friends over pints about how awful Linx is, and how both are {{He Man Woman Hater}}s.
* The BOSS and Stevens in "[[Recap/DoctorWhoS10E5TheGreenDeath The Green Death]]" are very homoerotic. The BOSS calls Stevens things like 'my little Superman' and Stevens' subplot is played very much like him dumping an abusive husband. The novelisation ramps up the subtext by having The BOSS quote Oscar Wilde and sing the Wedding March before asking Stevens, "Do you, Stevens, take this computer..."
* In "Cabinet Of Changes", Philip Purser-Hallard's sequel to ''The Blue Angel'', the Blue Angel version of Compassion ends up with the Blue Angel version of Romana. (It was published in a charity anthology, so not sanctioned by the BBC, but Purser-Hallard is a Who author for licensed books as well.)
* George Litefoot in Big Finish is AmbiguouslyGay. At one point he talks fondly of a lost love, without specifying the person's gender, in a way that rather strongly hints at his love having been male. In a later audio, in which everyone is talking about very personal and emotional moments, he recounts a story of trying in vain to impress a classmate named Ralph while at university. He's the first to recognise that one of the villains they encounter is gay, and explains to Jago that this is a case of the love that dare not speak its name -- as well as stating that he hopes the love may one day not be a taboo. He's quick to acknowledge when young men who cross their path are handsome, but doesn't seem to notice the women at all. He shelters Ellie in his house without even considering the social implications of an unmarried woman living with him. And his encounter with [[spoiler:fake]] Music/MauriceRavel (as well as the... more complicated situation between Ravel and the villain of the week) is really, blatantly romantic. Additionally, his description of the Doctor in "The Jago & Litefoot Revival", complete with emotional music in the background, speaks volumes.
* The Twelfth Doctor in "Smile" remembers once meeting an emperor made of algae. He looks wistfully out a window. dramatic music playing, and says, "he fancied me...", taking a few seconds to get back into his conversation with Bill.