Cloud Cuckoo Lander: Shafer acts this way, though he is unquestionably the best analyst in CIA. Whether he's that weird or he wants to mythify himself is beyond everyone.
Deconstructed supremely dark in form of Mohammed Fariz, an inmate of the Midnight House. Both his fellow jihadi inmate and American prison interrogators consider him to be crazy, and so no one pays attention to what he's doing. He ends up cutting his inmate to eighty-five bits and then slashing his own neck. The bleeding is so bad that the interrogators need waders to get in.
Contrived Coincidence: In Shadow Patrol, it just happens that Talib warlord Amadullah Thuwani's half-brother is Miteb, a Saudi prince whom Wells worked for in Secret Soldier. But better that than Ass Pull character.
A CIA team is preparing for an extraction mission to North Korea:
Kang (preparing a satellite image of North Korea): And that's North Korea. Dead as a whatever.
Beck: The good citizens of the Democratic People's Republic don't need the corruption of the outside world.
Kang: Yeah. Like food.
The Determinator: Wells. Most notably in Faithful Spy, where he's infected with plague, and in the Ghost War, where he's tortured in Chinese prison.
Downer Ending: The end of Midnight House. Wells has been made a fool by Vinny Duto so badly that he quits CIA.
The Dragon: Yusuf to Nasiji, Francesca to Lautner.
Driven to Suicide: Rachel Callar. The moment she saw what Mohammed Fariz had done and become because of the Midnight House, she breaks.
Driving Question: What happened in the Midnight House? And who is Stan in Shadow Patrol?
Earn Your Happy Ending: The Faithful Spy runs on this trope. For ten years, Wells lives undercover in the backwater of Afghanistan. When he returns to America, his mother was dead, his wife remarried, and his son doesn't know him. He couldn't adjust, his faith in Islam wears off, and his closest confidant Exley is trapped by her job. Even worse, neither CIA, who suspects him a traitor, nor Al Qaeda, who suspects him an infidel, trusts him. And then he gets infected with plague...But in the end, everything's worth it for Wells, for when he opens his eyes, there she is.
Most notably in Faithful Spy. Bin Laden asks Wells whether Hoover Dam is a great symbol of America. Wells says no. Nobody, not even Wells, knows how much credit he deserves for the fact that Hoover Dam is still in one piece.
This bites Wells in the ass in Midnight House. Fred Whitby threatens to reveal Wells' murders in Moscow in order to stop Wells' private investigation. When Wells fires back by taking credit for saving Washington DC from nuclear weapon in Silent Man, Whitby says Wells cannot reveal it without creating national hysteria.
Hannibal Has a Point: Amadullah is a stone-cold Taliban guerilla leader who moonlights as drug dealer. At the same time, he is tired of having foreigners making his homeland a battlefield of their own business. If Americans just leave, he and his fellow Pashtuns will make sure that al-Qaeda can never return to Afghanistan. Too bad Americans don't understand.
Amadullah: They didnít belong in his country any more than he belonged in America.
Kowalski. He is an amoral man who profits from dealing weapons to all sides in a war, but as shown in Silent Man and Secret Soldier, he does the right thing sometimes. In Silent Man, he give Wells a name of a terrorist nuclear network because he can't stand seeing cities like NYC gone for some religious tales. In Secret Soldier, he connects Wells with Abdullah, a moderate king of Saudi Arabia whom he regards better than the rest of the royals.
Unlike other ultra-patriot killers, Wells is not an assassin. He feels remorse when he kills those he has no problem with, and he always remember the people he kills. Only one caveat: he keeps killing anyway. It's part of his business.
Unlike other super-charming spies, Wells is not a womanizer. He is attached to one woman only, never takes up one-night stands, and feels genuine regret when his significant others chose to leave him. Only one caveat: Women still love him. He's just so handsome.
Unlike other Obstructive Bureaucrat, Duto is not one-dimensional. He protects people who protects his position. He has been kidnapped in the field and shrugged it off as easily as real soldiers might. Only one caveat: He's still arrogant, and you still can't trust him.
It's Personal: Deconstructed in the first arc of the Silent Man. After an attack on him leaves Exley severely wounded, Wells goes to Russia alone to take on one of the masterminds behind the attack, ignoring the advice from his Obstructive Bureaucrat boss Duto to wait for evidence. In a stock spy novel he would have succeeded. He ends up killing pawns who got nothing to do with the attack, missing the real mastermind, and needing to apologize to Duto to avoid prosecution.
Jurisdiction Friction: again, Midnight House, CIA versus ODNI. CIA wants the truth of Midnight House comes out and ODNI doesn't.
Khadri's plan in Faithful Spy. by car bombing Los Angeles and assassinating an ex-Pentagon top dog, he attempts to occupy CIA as long as he can until he can launch his two-pronged master plan: dirty-bombing Times Square and then plague-spreading New York subways.
Lautner's plan in Shadow Patrol. by dealing drugs with Talib warlord, he attempts to build his cred high enough so the Talib warlord agrees to have a private meeting with him, where he gives the warlord SAM to shoot down CIA plane.
Married to the Job: Wells. His first marriage and his engagement with Exley end because of this.
Memetic Badass: In-universe, in the aftermath of Faithful Spy. Though realistically, by fourth book it fades away. By sixth book, nobody recalls Wells on the top of his head.
The Mole: a subplot in Ghost War, a major plot in Shadow Patrol.
Nakama: Wells, Exley, and Shafer. Duto even lampshades this, calling them the Three Musketeers with us-against-the-world thing. Exley's out by the end of Silent Man, Wells quits CIA by the end of Midnight House.
The New Russia: a chapter in Silent Man. Wells despises it so much that, if the choices are between nightclubs of Moscow or piss-poor mountains of Afghanistan, he'll return to Afghanistan.
Nice Job Breaking It, Hero: by killing government-affiliated mercenaries in Russia, Wells makes it impossible for the CIA to investigate the attack on him and Exley.
Noodle Incident: In-universe. Just exactly what happened in the Midnight House?
Not So Different: Francesca screams this to Wells as they are fighting. But Wells knows better.
Francesca: You think you're any different than me, John? That what you think?
Yeah, somewhere on the way, you stopped caring who you killed.
Lawyer-Friendly Cameo: Averted in the Secret Soldier. Abdullah, the king of Saudi Arabia, appears as himself and serves as a major character.
Reality Ensues: Subtly, about Wells and Exley's relationship. In the Faithful Spy, their attachment resembles Romeo and Juliet's, and in the end they do get together. But in subsequent books, now that they move in and live together, they have to deal with each other's strength and weakness.
Supporting Protagonist: The Silent Man is overloaded with these. You have Grigory, a scientist who helps with the warhead theft; Bashir, an doctor who transforms the warhead into a working nuclear bomb; Kowalski, an arms dealer who tries to stop his feud with Wells by selling out a jihadi involved on the warhead theft; and Wells, who would never have heard of the nuclear plot if Kowalski hadn't tried to assassinate him and his girlfriend. The real protagonist of the book? It's Sayyid Nasiji, the Villain Protagonist.
Ultimate Job Security: Zig-zagged. After the Faithful Spy, Duto rewards Wells and Exley and Shafer his CIA director-level credentials, but puts them outside official chain-of-command of Langley. This means that our trio have blank check on whatever work they do, but one mistake and they are fired.
Up to Eleven: Berenson is as nice to Wells as Joss Whedon to Buffy. Just how much mental torture Wells has to pass through? Being infected by the plague? Tortured by Chinese prison guards? Left by his fiance? Played by his boss? Shooting an incapacitated enemy in the back? Having to kill fellow Americans?
Villain Protagonist: Sayyid Nasiji in The Silent Man. The whole novel revolves around his plot to nuke America. Of course, he fails.
Villain Title: The Shadow Patrol. It refers to a sniper duet that goes rogue in Afghanistan, Wells' ultimate enemy in the eponymous book.
Well-Intentioned Extremist: Li wants to purge corrupt ministers in Chinese leadership so Chinese nation can achieve greater prosperity. Only one problem: he does so by pushing China to war with America
What, Exactly, Is His Job?: In a pleasant twist, Wells asks this to himself. After the Faithful Spy, there isn't much he could do in CIA. Sure, he saves America once every year so far, but he doesn't have a daily job.
What the Hell, Hero?: Wells gets so many in Silent Man. From Rosette, Shafer, Duto, Kowalski, and Exley.
World Half Full: Wells has issues with his faith, relationship, and politics. And yet he still trusts that what he's doing is right.