It's one yearlater.The Master is the supreme ruler of the planet. Most people have spent this year in slavery (or dead) while the Master forces them to build a space fleet of makeshift (yet deadly) rockets to start a new age of space conquest and terror. Meanwhile, Martha Jones has been Walking the Earth, picking her way amongst the ruins, and following the Doctor's last instructions, looking for the four segments of a weapon that can allegedly kill the Master (permanently). She also discovers that the Toclafane are mutated remnants of the humans from the end of time.Meanwhile, the Master has made Martha's family into his personal slaves. He's also got Jack chained up as a toy to kill over and over. He plays with the Doctor for a bit while singing along to the Scissor Sisters, then uses his laser screwdriver to make him age extra centuries, turning him into a shriveled homonculus.Martha's returned to Britain, where she tells her story one last time and then is captured by the Master's Mooks. Up aboard the Valiant, the Master makes her Kneel Before Zod and prepares to kill her while a clock starts the final countdown to launch his war fleet across the universe.Then Martha laughs at him. Come on, she says, Plot Coupons? Seriously? And the Doctor asking someone to kill? No, what she was really doing was telling everyone about the Doctor. Thanks to Martha's stories, and using the Master's global countdown as a timing guide, the whole Earth manages to think the Doctor back to health and youth with a feedback effect through the Master's own mind-controlling cellphone satellite network, keeping people under his influence. The Master absolutely freaks out at this brutal turn of events, and after ordering the Toclafane to kill everyone he teleports away, followed (and soon captured) by the Doctor. Jack manages to sneak by the Toclafane and destroy the Master's paradox machine, which reverses time to exactly one year ago, with everyone's memories neatly wiped and all the mutated humans having disappeared from the present day. But everyone in the "eye of the storm" — including Martha's family — keeps the memories of everything they've seen.The Doctor attempts to stop everyone from killing the Master, since being a Time Lord he sees it as his job to deal with him by keeping him prisoner in the TARDIS. (Plus, evil or not, the Master is the only other Time Lord left to keep him company.) Suddenly the Master's wife shoots him. The Doctor urges the Master to regenerate the damage, but the Master smugly refuses to, and dies in the arms of a wildly sobbing Doctor, leaving him once again all alone in the universe.The Master's corpse is burned. Martha's family remains deeply traumatised. The Doctor puts a stop to Jack's vortex manipulator; "I can't have you walking around with a time travelling teleport. You could go anywhere, twice. The second time to apologise." Jack leaves because he misses Torchwood Three, but not before telling the others that he's very slowly aging into something unknown, and that his nickname was once "The Face of Boe". What. He dashes off to go rejoin Torchwood. Also, Martha finally understands that the Doctor will never return her affections. She hands him her phone, as she realises that she may need his help again some day.Meanwhile, at the Master's funeral pyre, a mysterious woman removes a maniacally laughing ring with Gallifreyan symbols on it. Is the Master not dead after all?As The Doctor sets off for his next adventure, he gets a rather rude surprise. A ship. Crashing straight through the side of the TARDIS. The name on the ships life preserver? Titanic...
After the End: Most of Earth. A short bit in the intro shows that it's bad enough that travelers from other planets are officially advised to avoid the place entirely.
Broken Bird: Lucy has clearly fallen off the deep end in the last year; she is noticeably skinnier and hardly talks. Considering the fact that she had seen the end of the universe first-hand and the most likely disturbing creation of the Toclafane, can you really blame her? She's also bruised and it's implied the Master has grown bored and started assaulting her.
And Jack; despite being brutally tortured by the Master for a year and later gunned down by a squad of soldiers, his clothes haven't a drop of blood on them.
Can't Spit It Out: Subverted; Martha comes as close as she'll ever get to telling the Doctor she loves him, and even though she doesn't say the words it's clear the normally Oblivious to Love Doctor knows exactly what she's on about.
Martha: I travelled across the world — from the ruins of New York to the fusion mills of China, right across the radiation pits of Europe; and everywhere I went I saw people just like you living as slaves.
Cruel Mercy: The Doctor's relentless attempts to forgive and rehabilitate the Master probably weren't intended this way, but the Master views them as worse than death.
Deus ex Machina: A glaring example. A satellite network which was used for subtle mind control by the Master is suddenly capable of giving the Doctor superpowers — telekinesis, regeneration (not talking about that kind), de-aging, flight and a force-field — provided everyone in the world thinks the word "Doctor" at the same time. This one comes with consequences: Martha's family, being aboard the Valiant, were at the eye of the storm. The Year That Never Was still happened for them.
Double Meaning Title: The title refers to the Master's plan to rule Earth as the last Time Lord (with the Doctor out of commission), but also to his decision to let himself die so that The Doctor will have to live out the rest of his life as the Last of His Kind. OK, neither plan really works out, but still...
Fate Worse than Death: The Master considers death preferable to being imprisoned by the Doctor, hence why he refused to regenerate after getting shot.
First Gray Hair: Captain Jack Harkness is immortal and apparently unaging, but at the end of the episode he mentions having found a grey hair, and theorises that he is aging, just very very slowly.
Forced to Watch: The Master made Martha's family watch as he burned down Japan. Small wonder Francine still wants him dead after the paradox machine is destroyed.
Gotta Catch 'Em All: Subverted Trope. Martha talks about having to travel around the world to collect the four hidden pieces to a gun that could kill the Master and prevent him from regenerating. When the Master catches her and reveals that he knows her plan, she laughs at him and says, "You really believed that?" Turns out the whole thing was a bluff and her actual plan was something else altogether.
Hoist by His Own Petard: The Archangel Network. The Doctor uses that year to tune his alien physiology to the frequency of the Network, just like an old mystic.
Humans Are the Real Monsters: The Toclafane are the future of humanity, who turned themselves into cyborg Psychopathic Manchildren in a desperate attempt to survive the collapse of reality. And why are they slaughtering their own species? Simply because it's fun.
Internal Homage: The revelation regarding the Toclafane's origins and its aftermath mirrors what happened to the First Doctor in "The Tenth Planet". In it, Earth's sister planet, Mondas, returned with mankind's dark mirror, the Cybermen, who have replaced their organic limbs and organs with mechanical ones in a bid to survive indefinitely. This knowledge ends up knocking the aged 1st Doctor out of narrative (this was caused by Hartnell's failing health), just as the decrepit 10th Doctor spends most of this story in dog kennel and cage, respectively.
Load-Bearing Boss: The TARDIS has been reconfigured into a Paradox Machine. Jack breaks the Paradox by shooting at the console.
Madness Mantra: "We shall fly and blaze and slice! We shall fly and blaze and slice!"
Meet the New Boss / Same Story, Different Names: The Toclafane's origin story mirrors that of the classic Cybermen in "The Tenth Planet". In it, the Earth's lost "sister planet" of Mondas returned along with our evolved cousins, who turned out to be metallic fossils of their former selves. Those events proved too much for the 1st Doctor, who died of exhaustion. Ten fares a little better here, though he still ages a lot; and his faith in humanity is once again shaken.
No Ontological Inertia: So the Master "cannibalised" the TARDIS into a Paradox Machine? So Doctor, if it was really that bad, do you want to explain how you managed to get her fixed so incredibly quickly? The following special "Time Crash" implies this is about as complicated as changing the desktop theme of a computer.
The Power of Friendship: Martha escapes the Master's takeover of Earth and spends one year traveling the world telling everyone about the doctor and how they're supposed to say (and believe!) "doctor" over and over during an onconming countdown. When said time arrives, everyone in the world doing this (even the Master's human followers and his ownfreaking wife) gives the Doctor the strength he needs to overpower the Master and undo all his evil.
Reality Ensues: The Doctor talks Francine out of shooting the Master and declares he's got someone to care for — and enter Lucy. BANG.
Reset Button: Wrecking the Paradox Machine resets the timeline, undoing most of the Master's atrocities (although President Winters is conspicuously still dead).
The Doctor: You're my responsibility from now on. [...] The only safe place for him is the TARDIS. The Master: (smirking) You mean, you're just gonna... (the smirk fades) keep me? The Doctor: Mm. If that's what I have to do. (to his friends) It's time to change. (the Master rolls his eyes)
Sequel Hook: The hand that takes the Master's ring. Russell T Davies even joked that it was "the hand of the Rani". Notable as this was initially designed as purely a generic hook with no actual plans to follow up on it. RTD didn't want to use the Master again, but put it in as a way for his successor as show runner to use if they so desired. Then he changed his mind and used it himself at the end of his run.
The Toclafane bear an uncanny resemblance to the spheres from Phantasm, right down to being powered by the brains of the creator's human victims.
The scene where The Master is burnt on a funeral pyre by the Doctor is reminiscent of Luke setting ablaze Darth Vader's armour at the end of Star Wars: Episode VI.
A woman with red-painted fingernails picking up the Master's ring as his laughter is heard in the background is one to the end of the 1980s Flash Gordon film.
Status Quo Is God: The Master's year of terror is undone, and the Doctor is still the last of his kind (until the next time the Master shows up).
Super Mode: The Doctor temporally gains an upgrade when he's revived by the world, gaining the ability to float in mid-air and telekinesis.
Taking You with Me: The Master tries to do this when the Doctor and Martha foil his plans by detonating his fleet of rockets (thus triggering an Earth-Shattering Kaboom). However, the Doctor points out that the Master would never take his own life, and convinces him to surrender.
Time Bomb: The Master never could resist a ticking clock.
Villain-Beating Artifact: Subverted. The episode features Martha Jones spending a year trying to locate a weapon divided into four parts that can defeat the Master, only to reveal at the very end that the Villain-Beating Artefact was a ruse to distract from Martha's real goal.