Aborted Arc: The whole thing with Cyrus being a secret evil mastermind seems to have been dropped in exchange for Hollis Doyle. Cyrus is still morally ambiguous, but no more so (or at least not much more so) than Olivia at this point.
Ambition Is Evil: Mellie. She does not take too kindly to Fitz wanting to willingly give up the presidency, demands to be included in security meetings, and there is no love lost between her and Fitz. She also clearly has designs on building a formidable political career of her own once Fitz's term comes to an end. She also falls out with Olivia as she believes the Amanda Tanner scandal could have been prevented if Olivia had not broken off her affair with Fitz.
Angst Coma: Olivia briefly enters one in "Truth and Consequences."
Sally Langston's husband to a somewhat lesser extent.
The Artifact: Virtually all of Olivia's team besides Huck is now more-or-less useless to her other than an extra pair of hands to help sort through files. The dark centered plot the show is headed makes their wacky character shticks rather out of place, and only Huck has any knowledge or capability that doesn't leave him completely over his head.
Olivia's "gut" was something that was frequently mentioned during season one, and how her intuition is always right. At least it was long enough to prove to the audience that she is quick thinking and a very good judge of character. But by season 2, it is pretty much only mentioned when discussing how "her gut is broken" these days. By season 3 her magical intuition is no longer referred to, and her near godliness has been thoroughly de-emphasized.
Olivia's "gut" returns in "Ride, Sally, Ride." Fitz overrides it to pick Andrew Nichols as his VP running mate. It turns out Olivia's gut was right even if she didn't know why: Andrew is secretly in love with Mellie.
As You Know: Averted and invoked in "Hunting Season." When Cyrus shows Fitz that Olivia and Senator Edison Davis are meeting in public, he starts to say "Didn't they..." Fitz snaps "I don't need a history lesson, Cyrus." Later on when talking to Olivia, Fitz says Edison used to be Olivia's fiance... which Olivia would obviously know.
The Atoner: Olivia wants to do right by her clients, but especially the ones who are women caught in infidelity scandals. Those hit a little close to home for her.
Bedmate Reveal: At the end of "Hunting Season," David and Abby. It is revealed after the two... uh, finish.
Beta Couple: Starting in season three, David and Abby. They seem to handle extreme situations better than the other couples.
Beware the Nice Ones: Quinn, again. Olivia too, if Abby's story of Olivia beating in her abusive ex-husband's kneecap for her is true.
Bitch in Sheep's Clothing: It takes six episodes, but First Lady Mellie Grant reveals herself as this, lying to the entire nation about a miscarriage to save her husband's campaign. It's interesting, however, that the sheep part isn't unnatural for her, as she does have issues of her own, and seems to be more than a little Troubled, but Cute.
Blackmail Is Such an Ugly Word: In "State of the Union," Olivia does not want to work for the White House anymore. But Cyrus deposited money into her account to get a popular married couple to show up at the State of the Union. Cyrus just sees it as paying Olivia (way) in advance, and he will notify the IRS if she doesn't do the job.
David attempts blackmail in a later episode in order to counter the judge getting bribed, and it does not go as well. David blackmailed with information about a drunk driving homicide so the judge would uphold a contentious gun control law. The judge agrees, David is a hero, then the judge commits suicide.
Break His Heart to Save Him: Invoked by Olivia to save *both* David and Abby from Hollis Doyle without either of them knowing about it. She had Harrison do it and didn't tell him why. Whether Harrison did it out of loyalty to Olivia, his friendship with Abby or to get a bigger office is nebulous.
Burger Fool: A popular fast food chain called "Gettysburgers" is mentioned often, with their food and special deals named after people and events of The American Civil War. The fourth season revealed their employees dress like Civil War soldiers, but only in Union blue.
The Bus Came Back: After roughly a season of not being seen, Billy Chambers is revealed towards the end of season two to have been "Albatross", a mole that has been causing the Grant administration problems for most of the season.
Leo Bergen made a surprise reappearance in Season 4 after the end of Season 3.
Call Back: In "Enemy of the State" Abby says she would follow Olivia "off a cliff." In "White Hat's Back On" Olivia tells Fitz that her team followed her "off the wrong cliff."
Call Forward: In "Hunting Season", we see Huck has a collection of watches. The importance of this collection is not revealed until flashback in "Seven Fifty Two." The watches are trophies from people he tortured and/or killed.
Calling the Old Man Out: Fitz attempted this with his father, Big Jerry, in flashbacks about the month leading up to the election. But Big Jerry's "The Reason You Suck" Speech comeback was much harsher, and part of the reason Olivia agreed to go along with the election rigging: She didn't want Fitz to feel bad about himself if/when he lost the election.
Call to Agriculture: Averted in the first season. Cyrus works in his garden on Sundays, his one day off. Later in the episode he says he hates working in his garden on Sundays.
Casanova Wannabe: Stephen, though he seems to have mostly settled down. He still has an interesting past.
Cassandra Truth: Huck to Olivia in a flashback in "Guess Who's Coming To Dinner."
Huck: I was a trained assassin for secret office of the CIA on US soil called B6-13 run by a man called Command in a paper company that's not really a paper company. It's called Acme Limited, but really it's called Wonderland. Welcome to Wonderland, son. Then they put me in a hole, and then I wasn't so good at my job anymore. And then I wasn't in Wonderland anymore. I was here, but I can still I can kill a man with very little effort and a lot of joy, but I try not to. Okay?
Olivia: ...Is there medication you should be taking, or anyone I should call?
Category Traitor: Control/Rowan/Eli comes close to calling Olivia this for siding with Fitz and Jake, who are both white, against him. He calls them her "clan of good ol' boys." It is a lot of hypocritical, self-serving nonsense, as Olivia is angry at her father for killing her friend Harrison, who was black, as well a lot of other people. Also, Rowan was all right with Olivia dating Jake... before Jake found out Rowan had killed Fitz's son.
City of Spies: Washington DC is one. Normal people on the street could be working for an unofficial branch of the CIA that operates on American soil. Or could be freelancing for the Chief of Staff.
The Conspiracy: A large part of Season Two's backstory involves one including Olivia, First Lady Mellie Grant, Cyrus Beene, Hollis Doyle, and Supreme Court Justice Verna Thornton. All five of these people were part of Fitzgerald Grant's election campaign, and all worked together on an election rigging conspiracy for various personal reasons: Hollis for the business connections, Mellie to be First Lady, Cyrus to be the President's adviser, and Verna Thornton to get on the Supreme Court. Olivia did it for Fitz. Hollis Doyle's company Cytron rigged several voting machines in a small county in Ohio named Defiance; the machines gave two-thirds of the vote to Fitz no matter how the county actually voted. Quinn/Lindsay Dwyer's framing was related to this conspiracy because her boyfriend, a journalist, was beginning to discover the truth and the fact that Cytron was involved in the scam. Thus, Hollis arranged for Lindsay's boyfriend to get blown up with a bomb and for Lindsay to get framed for it. Olivia, however, could not bear to see Lindsay's life be destroyed over something she felt was her mistake, so she arranged for Huck to abduct Linsday and give her a new life as Quinn.
The conspiracy may not have been well-hidden as they thought. Governor Reston, the opponent in the election, hints he knows about the conspiracy but can't prove it in "All Roads Lead to Fitz." A Rewatch Bonus of that episode after the conspiracy is revealed shows Reston probably wasn't angry over a simple "Soft on crime" campaign ad.
A second conspiracy is revealed in the first half of Season Four. It involves getting Fitz to get America involved in a war in West Angola. Two teenage girls are killed to hide the conspiracy, bringing in OPA's involvement. The plan includes blowing up the Vice President's limo and forcing Cyrus to resign as Chief of Staff. When these do not work, Olivia is kidnapped. Vice President Andrew Nichols asks Fitz how far he would go to get back something he loved, ending with "How are you liking that war now, sir?"
Contrived Coincidence: It can be argued Huck seeing and recognizing Charlie on a tape falls in this category. This leads to Huck realizing Amanda is dead, as Huck and Charlie were once co-workers.
The Chick: Abby Whelan (when she isn't an alternate Heart).
Fourth Wall Psych: Jake Ballard does this at the end of "Top of the Hour." He appears to smile knowingly at the audience. He's actually smiling knowingly at the cameras he planted in Olivia's apartment.
Framing the Guilty Party: The woman in "Hell Hath No Fury" is doing this. He didn't rape her; he raped her best friend, which eventually triggered her suicide.
Futureshadowing: "Seven Fifty Two" has flashbacks of when Olivia first met Huck. Fitz is on a magazine cover with the tagline "Is this man our next president?"
Gay Conservative: Sullivan St. James in episode 1. Cyrus Beene is revealed to be this in episode 4.
Genre Shift: Shonda Rhimes' plan all along was to hook the audience with a soapy, case-of-the-week first season, before amping up the serialization and political thriller elements in season two.
Season 3 is doing this again with a lot of it's plot shifting towards a Spy Drama.
Glad-to-Be-Alive Sex: In "The Last Supper," Mellie and Andrew Nichols after Andrew is almost killed by a car bomb.
Gone Horribly Right: In season three, Cyrus' plan to expose Sally Langston's husband's homosexuality results in the disintegration of Cyrus' marriage (thanks to James' infidelity) and Sally murdering her husband.
Green-Eyed Monster: President Fitzgerald Grant veers into this territory in the season two episode "Hunting Season." He finds out Olivia was talking to Democratic Senator Edison Davis who used to be Olivia's fiance.
Sally Langston isn't particularly thrilled to find out her husband is gay and unfaithful.
Olivia: Had an affair with President Grant during the campaign, assisted in rigging a national election in his favor, and covered up "Quinn's" real identity because of her accidental involvement in that rigging conspiracy, even conspiring with a Supreme Court justice to get her acquitted.
Abby: Was married to a famous U.S. politician until she ran away. Their marriage had a history of domestic abuse and he's still searching for her.
Harrison: Convicted of insider-trading, served serious jail time. He was also involved in something called Clearwater with Adnan Salif.
Stephen: Was a hotshot lawyer, then had a breakdown in the middle of a trial where he was defending a large company that had destroyed a few lives through their chemical manufacturing.
Quinn: Her real name isn't Quinn, and she didn't exist in that identity until two years ago.
As season two reveals: her real name is Lindsay Dwyer, she was framed for a bombing that killed seven people, and the conspiracy surrounding why stretches to not only Olivia, but the Supreme Court and the national security of the United States. This was further explained in "Happy Birthday, Mr. President": Hollis Doyle, the head of Cytron, rigged the explosion to get rid of evidence that Cytron helped orchestrate the rigging of the presidential election in Fitz's favor. He framed Lindsay Dwyer for the bombing. This did not sit right with Olivia, so she and Huck spirited Lindsay away and gave her a new identity as Quinn Perkins..
Huck: His dossier is apparently thicker than most spy novels, most of it is redacted, but he has CIA/espionage/military training as an assassin and Olivia trusts him to break a dictator's wife and children out of the embassy with only five minutes' leeway. He's also spent time homeless and suffering from PTSD, begging on the DC subway, which is when Olivia found him. Also, he probably has an ex-wife and child living somewhere in DC.
There's also the surprising and villainous depths to Cyrus Beene - he's a Gay Conservative, and married to a much-younger man.
B613 has an agent stationed in the White House to keep Command in the loop. Who would have predicted that it would be Tom the Secret Service agent?
Hide Your Pregnancy: Kerry Washington (Olivia) is pregnant in season 3, however that was not written into the show (obviously).
Quinn, when she dated a reporter that she got to know when he wanted information that she had. Her surprise after he died that he was still working on the case was especially baffling for someone who apparently has so many secrets herself.
Speaking of him, Gideon was hit with his in episode 6 - When confronting the person behind the majority of the shadiness in the story you're investigating, it's always best to do so in a public place or even to not let them know all that you know. But should you do both of these things , don't turn your back on them. It can only end one way.
Ignored Enamored Underling: Revealed to be the case of California Governor Andrew Nichols, who used to be Fitz's lieutenant governor: He's secretly in love with Mellie.
In-Series Nickname: Charlie likes calling Quinn "Robin." In "Like Father, Like Daughter," Fitz has an entire list for Mellie: "Drunk Mellie, Smelly Mellie, Screw-Everything-To-Hell Mellie, and Crybaby Mellie, and Eat Everything That Is Not Nailed Down Mellie."
Keeping Secrets Sucks: Olivia can speak from experience. And she might not be as good as it as she thinks. People know she had a secret romance during the campaign, but not with whom. Jeannine Locke tells her in 3x02 that many White House employees knew President Grant was having an affair, but not with whom.
Knight in Sour Armor: Olivia and Cyrus, who both do/condone horrible things in service to clients and the President, respectively.
Albeit accidental, as she thought Amanda was a manipulative Fake Cutie, when she reminded her rival (Amanda) of her mother's psychotic break and menaced to use it to end her career, the result was a really creepy Olivia.
Cyrus has plenty of those moments even before he proves to have been Evil All Along.
If the first two episodes of season two are anything to go by, David's the new target of Olivia's dog-kicking.
Knee-capping: Olivia, apparently, to Abby's abusive husband. With a tire iron.
Large Ham: You could make arguments for a few characters but Rowan Pope has to take the cake.
Manipulative Bastard: Olivia is one, and most of her team live on the verge. Fitz refuses to be one, Cyrus is proud of being this, and Mellie Grant has shown herself quite capable of it.
The Masquerade Will Kill Your Dating Life: With Huck, [[spoiler: after being reunited by Quinn with his family at the end of Season 3, he attempts to patch things up with his ex and her son between seasons. In Season 4 we learn that he told her the truth about his involvement with B-613 as a sign of good faith, but not only does she not believe him, she has repeatedly called the cops on him, and ultimately ambushes him with a shrink.
The McCoy: Quinn and Abby both serve as this for the rest of the team.
Never Heard That One Before: In "A Door Marked Exit," Rowan/Eli goes on an epic rant to Fitz about how Fitz is a spoiled, ignorant child. Fitz doesn't say anything, but you get the feeling he's been hearing this ever since he WAS a spoiled, ignorant child.
Not Evil, Just Misunderstood: Amanda Tanner. Olivia's third client (not counting the little girl herself and her earlier clients, which includes the president) when accused of murder.
Not So Different: Olivia attempts this with Mellie in "We Do Not Touch the First Ladies." It fails. Olivia thinks Mellie had an affair with Andrew Nichols. While Andrew is in love with Mellie and Mellie reciprocates on some level, they've never had sex. Until "Kiss Kiss Bang Bang," when they do.
Olivia can lose her stoicism in cases involving infidelity.
Obliviously Evil: Cyrus, initially. Not anymore, as of season 3: "You must've missed the '666' printed on my forehead."
Only Sane Man: Abby sees herself and Harrison in that role. How right she is is up to debate.
Only Smart People May Pass: In the Pilot, Olivia and the gang uncover two "secrets" - the gay soldier who wanted to run for Congress and the President's philandering. Since the soldier was meeting with his lover in a public place (bar/restaurant) and they enlisted the help of a security guard to get a tape of the two of them, it didn't seem very hard to uncover the "secret" or that it's likely to be secret very long. Similarly, the President starts making out with Olivia in the Oval Office having just pointed out there's a camera in the ceiling and is then interrupted by his Chief of Staff. If the President is that careless, how exactly has he not been caught before (the CoS makes it clear he didn't know)?
Olivia's affair was not as secret as they thought. The Secret Service are very discreet, but Jeannine told Olivia that people at the White House knew Fitz was having an affair, but not with whom.
In Season 3's episode "A Door Marked Exit," we had two gigantic ones: one in a flashback from Sally to her husband and her husband right back at her, regarding his cheating and orientation and his ability to influence her political career before she stabs him in the back, literally and one from Olivia's father, Eli/Rowan, to Fitz regarding Fitz's perceived spoiled childhood and not being good enough for Daddy's little girl. While Fitz has him locked in a room in the Pentagon effectively powerless, no less.
Olivia delivers a blistering one in season four to a couple who tried to blackmail the president over a sex tape of his daughter. It doubles as a Moment Of Awesome both for the content of the speech and because they are immediately cowed into doing her bidding.
Recruited From The Gutter: Huck was a government assassin who fled a Resignations Not Accepted situation. He lived as a homeless man on the subway where he rescued Olivia ( the daughter of his former boss) from some muggers. An arrangement was reached which ended with Huck working for Olivia as one of her Gladiators when she formed her own PR firm.
Red Herring: You had to have thought that CIA Director Osbourne was the mole they were searching for. "Snake in the Garden" has the character get killed off at the end, and it's revealed that they got the wrong guy.
Room Full of Crazy: David has this to see why Olivia is helping Quinn. So far he's figured out Quinn was framed for the bombing, as Olivia uses her powers for good instead of evil. At the start of season 4, he has a Storage Bin Full of Crazy. It contains all the B6-13 files Jake gave him. David has organized the files by Scary, Really Scary, and Crap-Your-Pants Scary.
"Rashomon"-Style: A flashback in Season 2's "Happy Birthday Mr. President" is expanded upon in a flashback in Season 3's "Kiss Kiss, Bang Bang." The first flashback has Olivia noticing an argument between Cyrus and James over the Inaugural Ball. The second flashback shows the argument from Cyrus' perspective, where James is angry Cyrus still sees him as a "dirty little secret."
Samus is a Girl: Done twice: Vice President Langston and with Harrison's former boss Adnan Salif who is also Harrison's former and current lover.
Seamless Spontaneous Lie: One unusually noble example was done by Andrew Nichols: When it was revealed Oxycontin was delivered to the governor's mansion, Andrew says he had the Oxycontin delivered because he hurt his back and thought getting a prescription would be seen as hypocritical given his strong anti-drug stance. It turns out Andrew is covering for Mellie, who attempted suicide with the entire bottle. Andrew saved Mellie's life and never told anyone.
Sequel Hook: Quinn's real identity and backstory are about to be revealed.
The end of season two: Olivia exits her apartment and is verbally assaulted by the media, who reveal that her name has been leaked as the President's mistress. She then gets into a car with Huck's former Jake's current boss, implied to be the head of the classified B6-13 CIA program, and says, "Dad?"
The "Fall Finale" of Season Four, "Where the Sun Don't Shine": Olivia is kidnapped to force Fitz to start a war on (or in) West Angola.
Sex for Solace: Implied to be the reason the president's daughter Karen sleeps around in season four.
Shell-Shocked Veteran: Huck reveals himself to be this, due to his CIA black-ops training. He and his other operatives were conditioned to torture enemies and eventually grew to like it. Huck wanted out and was trying to "get sober" while living homeless when Olivia found him.
The season two episode "Seven Fifty-Two" reveals that he has a wife and child, but after torture and sensory deprivation by the CIA he is no longer sure that his memories of them are genuine. He does, however, apparently remember seeing them while living homeless at a subway station; his son gave him money, with neither his son nor his wife apparently realising it was him. The episode title (which Huck repeats for almost the entire portion of the episode set in the present due to shell shock from a recent attack he suffered very similar to the sensory deprivation to which the CIA subjected him) refers to the time when this occurred.
Ship Tease: This is very briefly done in the flashback where Harrison and Abby first meet. Abby looks like she's about to start flirting with Harrison, until he mentions he has to meet his parole officer.
Cyrus uses "I saw Goody Proctor with the Devil!" from Arthur Miller's The Crucible, adding "Right here in DC!" to warn Olivia how a Sally Langston presidency will be.
Mellie likens Olivia to Cleopatra in "Icarus," but not in a good way. "I did everything but roll your whore up in a rug and unfurl her at your feet!"
In "A Door Marked Exit," similar to Batman Begins, someone finds out he's fired by being asked "Didn't you get the memo?"
At the start of "Randy, Red, Superfreak and Julia," Olivia is reading the novel Gone Girl and using the alias "Julia Baker," the name of Diahann Carroll's character on the TV drama "Julia."
Olivia is likened to Helen of Troy by Tom in "Baby Made a Mess." A bit of Fridge Brillance concerning the "Face that launched a thousand ships" line, after Olivia is kidnapped so Fitz will start a war in West Angola.
Jake stalking an apartment is intercut with Rowan/Eli prepares a glass of wine. Similar to Silence of the Lambs, Jake finds an empty apartment and Rowan/Eli is actually in Olivia's apartment.
Sympathetic Adulterer: President Fitzgerald Grant, perhaps. Sometimes the audience feels bad for him and Olivia, but other times, it's clear his infidelity is causing more problems than it's probably worth.
Tastes Like Diabetes: In "Baby Made a Mess," Olivia makes an absurdly cute campaign commercial with the ten-year-old daughter of a candidate for the senate. The candidate herself, while smart, isn't very telegenic.
That Man Is Dead: In "The Other Woman," Quinn comes to terms that her life as Lindsay Dwyer is over. Huck even tells her that eight people died in that bombing, not seven. In "Hunting Season," she becomes very insistent that Abby calls her Quinn, not Lindsay.
They Call Me Mister Tibbs: In "The Last Supper," Jake bitterly asks Fitz to call him "Captain Ballard," as they are not friends anymore. A bit of a Tear Jerker, as Fitz and Jake are probably the oldest friends on the show.
Three-Way Sex: A rather filthy tape involving the president's daughter Karen becomes a plot point in a season four episode.
Time Skip: There is a ten month Time Skip between "Nobody Likes Babies" and "Whiskey Tango Foxtrot." The Time Skip between the end of Season 3 and the start of Season 4 is two months. (The nice weather in Washington DC made it seem like more.)
Olivia's team will bend the rules all over the place but will generally refuse to break the law. They do seem to make an exception as far as Huck's hacking is concerned. However, in the season one finale they can't Take a Third Option and have to make a choice whether to destroy evidence in order to protect Quinn.
In 2.01, Olivia's last-ditch choice of getting Justice Verna to shut down Quinn's trial may have consequences.
Token Good Teammate: At the start of the third season, Olivia seems to be this to the rest of the team.
Torture Always Works: Apparently, it even works if you keep the subject's mouth duct-taped shut until he's past the point of being able to form coherent words.
The Unreveal: A minor example on episode 2.16 with Patient of the Week Sarah Stanner, who had an affair with Supreme Court nominee Murray Randall when he was a Harvard law professor fifteen years ago. Later, Sarah admitted to her husband that she slept with Randall two years prior, right around the time they had a second child, which infuriated him enough to demand a paternity test. When Olivia gave the husband the results, sealed inside an orange envelope, she told him that the results changes nothing. His marriage will need time to repair, and the knowledge of who's the biological dad won't erase that he's his second child's true father. Olivia's advice convinces him to rip up the envelope.
Billy Chambers has his girlfriend sleep with the president and follows it up with blackmail and murder so the 'right' person can become president.
Frequently used to justify the election rigging that made Fitz president. Mostly by Cyrus and Olivia, but occasionally also by Verna Thornton.
Very Loosely Based on a True Story: The show is based on the career of real life George H.W. Bush deputy press secretary/crisis manager Judy Smith, though obviously with plots far from the reality of the Bush 41 presidency meant to appeal to 2012 audiences looking for dramatic tension.
Wham Episode: "Defiance": President Grant and the press secretary get shot.
"Nobody Likes Babies": President Grant finds out the truth about the election rigging from Verna... right before he murders her, breaks up with Olivia, and more-or-less reconciles with Mellie.
"Everything's Coming Up Mellie" reveals lots and lots of secrets: Cyrus used to have a beard. And facial hair, too! Big Jerry raped Mellie and might be the real father of Fitz's son. Charlie tricks Quinn into killing a lead, recruiting her into B6-13. Sally Langston's husband is gay and interested in James. Fitz finds out Olivia's father runs B6-13. Olivia's mother is still alive.
"YOLO": James asks Cyrus for a divorce. Huck tortures Quinn for her betrayal of Olivia. Olivia's mother is genuinely guilty of as-yet-unspecified crimes against the Republic. Quinn is going to kill Command (AKA Olivia's father). Oh, yeah, and the Vice President murders her husband.
"We Do Not Touch The First Ladies": Mellie's rape at the hands of her father-in-law pushed her to attempt suicide, and it's heavily implied that the rape itself is ultimately the reason why her marriage with Fitz starting falling apart. Rowan has been working with Leo Bergen to ruin Fitz's chances of reelection. Quinn threatens Olivia with a gun. Adnan Salif is working for Olivia's mother. Tom is secretly a B613 agent who fills Command in on events in the White House.Oh, and Hollis Doyle is hanging around again.
"No Son on the Horizon": James had just decided to back off of working with David on the investigation of Sally's Langston's husband's death because, despite himself, he still loves Cyrus. It turns out, David hadn't set up the meeting; neither had James. They were set up by Jake, new head of B613; walks up to them, shoots the two women with them, camera pans off them, we hear a single shot, and cut immediately to black.
"Kiss Kiss Bang Bang": James gets Killed Off for Real by Jake, who is now forcing David to have an innocent man arrested and tried for the murder under threat of death. Olivia and the Gladiators find out, but have to keep it quiet from Cyrus to hopefully bring down B613. Quinn, who's still working for B613, has recently snuck into Olivia's office; the sloppy way she went about it, leaving video evidence that could be found when Huck taught her not to leads him to think she still is a Gladiator after all. And he ends up kissing her.
"The Price Of Free and Fair Elections": President Grant's son is dead. Maya Pope didn't kill him.
"Where the Sun Don't Shine": Olivia is kidnapped to force Fitz to start a war in West Angola. Elizabeth North and Vice President Andrew Nichols are part of the conspiracy.
Wham Line: The final line of "White Hat's Back On."
A whole bunch in "Everything's Coming Up Mellie."
Eli: Our daughter has been asking about you.
Charlie to Quinn: You belong to B6-13 now. Welcome to Wonderland.
Fitz (in flashback): You know, if it's a boy, he's going to want us to name him "Jerry."
"The Price of Free and Fair Elections"
Eli: "He took my child. So I took his."
"Where the Sun Don't Shine"
Andrew: “How are you liking that war now, sir?”
Wham Shot: The final shot of "A Door Marked Exit" has Maya (dressed in a white coat similar to Olivia's) tossing a burner phone into a trash can on the sidewalk... that is outside the gates of the White House.
What Happened to the Mouse?: As explained to Quinn in the first episode, sometimes we don't get all the answers. In the first episode we never did learn who the real killer was.
Xanatos Speed Chess: The entirety of Season 3 would appear to be this on behalf of Command/Rowan/Eli Pope, although it's unclear how much he either anticipated (thanks to his access to B613's intelligence) or instigated versus how much he planned on the fly. Regardless, the events of the season worked out well for him: his daughter got on that plane, the President owes him and is unlikely to interfere with B613 anymore, his most troublesome agent is out of the picture, and he got to torment his terrorist wife and kill her lover.
It continues to Season 4. Command/Rowan/Eli Pope takes advantage of Agent Bixby learning Secret Service Agent Tom was at Fort Dietrich, framing Jake Ballard for killing Jerry Grant. Rowan probably figured someone would learn about Tom being at Fort Dietrich eventually, and is using Bixby's discovery to get Tom to say Jake Ballard told him to kill Jerry Grant.