Flynn's Establishing Character Moment in the show - he pops up out of nowhere, thoroughly confuses everyone present (Baird and a couple of terrorists), walks Baird through disarming a live and ticking nuclear weapon while he disarms a booby trap on an ancient magical artifact's containment case and she engages in a gun battle with the terrorists, manages to count the shots one of them fires from an automatic weapon, and then leaves before anyone can get any idea of what's going on (disappearing while Eve's back is turned, naturally).
Flynn taking down Lamia with a makeshift electromagnet.
Baird ripping out the Minotaur's nose ring just to piss it off and then engaging it in hand-to-hand combat, buying time for Stone to steal a car and hit the Minotaur with it.
Earlier, Baird takes on the Minotaur with nothing more than her guts and her handgun. She wins.
Eve taking Santa's place to spread goodwill in "And Santa's Midnight Ride". To hear Santa talk, it should have killed her.
Stone got into a bar fight. On Christmas Eve. With Santa, AKA Odin, as backup.
Cassandra, under the influence of the title object of "And The Apple Of Discord", taking down Lamia in three moves.
Ezekiel taking the apple from under Flynn's very nose. He also deduces that it was Drake who stole the pearl from the Eastern Dragons, thus preventing a draconic war from breaking out.
Jenkins using every loophole and minor legality of the conclave rules to drag it on and keep Dulaque from calling a vote of no confidence on the Librarians.
An unintentional one for Evil Flynn, whose power-drunk ranting actually provided the perfect argument why the Library's artifacts must not be allowed to run loose. If just one such object of power can turn a heroic defender of the planet into a deranged megalomaniac who's more than ready to upset the apple cart for all the supernatural factions, how can they ever allow somebody who's already ambitious to usurp the Librarian's role?
Jamie getting a hold of the book in "And The Fables of Doom". Turning Stone into a kickass Robotic Huntsman, Eve into a ninja princess, and Cassandra into Merlin Prince Charming.
"I'm Amy Meyer. I've won every ribbon, every medal, every trophy that you've wanted since we were 5 years old. Do you really think I'm bluffing?"
Dulaque and Jenkins' sword duel at the climax of "And the Loom of Fate". What makes this even better is that Dulaque's alterations to the Loom have de-aged him to his prime as Sir Lancelot, while Jenkins is still an old man...and he still holds his own, even beating Dulaque.
Not only that, but he holds his own one-handed. Where's his other hand? In his pocket.
Alt!Cassandra is a Librarian who has mastered magic. She is treated like a queen by everyone in her reality. She had saved them from the dragons. She later does a summoning spell that pulls Alt!Stone and Alt!Ezekiel into her timeline.
Alt!Cassandra: Quiet, I'm doing math.
Alt!Flynn being able to save the day in the multiple other timelines due to the fact he has abilities none of the Librarians have.
Season 2
Flynn awesomely outmaneuvers Prospero in "And the Broken Staff." Flynn tells Prospero that he'll never tell him which tree is the Tree of Knowledge... at which point Prospero feints in one direction, and Flynn reacts as if to stop him. Convinced he's found the Tree of Knowledge, Prospero snaps a branch off to forge into a new staff, but then Flynn flings Zeus' Lightning Bolt from his jacket and incinerates the tree. From Prospero's view, the Tree of Knowledge has been destroyed, so he takes his leave of the Library since there's nothing left for him to gain. Flynn then reveals that the actual Tree of Knowledge is a different one entirely.
Eve snatched Prospero's pocket watch containing Ariel and dangles it over a cliff. When Moriarity claims that he can simply dive after it, she points out that Fictionals can still be defeated by something that happened in their story...and the other time he dove off a cliff didn't exactly end well for him. Moriarity can only concede the point, and tries a different tack.
Stone ripping into his father and telling him the truth about himself, which initially seems heartwarming.
Stone's Father: Why in the hell should I listen to you?
Stone: Because I'm a genius, pop. I'm a genius. I speak nine different languages, and I can read over a dozen more! I have honorary degrees at universities on four different continents! I'm the first one they call when they discover a new piece of art, and I'm the one they're scared to call, because I'm the best in the world at discovering a fake! And I didn't tell you, because I knew that you'd see anything less than chasing the family business as a betrayal!
Then revealing that his real father would never admit that he loved him, and drags both himself and the shapeshifter down a hole, towards the prison.
Stone: [whispers in the monster's ear] One more thing. My father would die before he ever told me that. [drags both of them into the hole]
Then the thing tries a Shapeshifter Guilt Trip, but Stone just punches it in the face anyway.
Stone: I know they're all you, so go ahead and bring on whoever you want!
Baird pulls a bit of Loophole Abuse in "And the Infernal Contract", turning the devil "Cess" into a human. Doubles as a Crowning Moment of Funny for his double-take.
Another bit of loophole abuse is that Cess states anyone trying to interfere with it will be killed...so who rescues the Librarians? Jenkins, of course.
Cess: It cannot kill what's immortal!
Jenkins: (winking) Now you're getting it.
In fact, when driving the point home, Baird says of Jenkins, "I know when you're facing an entrenched enemy, it's a good idea to bring a tank."
Stone figuring out that the primary portrait was a fake, realizing that the colors were too new looking at a moment's glance.
Prospero weaving Eve, Moriarity, Stone, Cassandra, and Jones into a narrative spell is awesome enough as it is. But what really takes the cake is when Flynn breaks all the others free...only for Eve to realize that he's under a spell too, but so subtle that he would never have realized.
How do Eve and Flynn get back to the future? They get Shakespeare to use his magic pen one more time, turning them both into statues until they hear Cassandra's voice, and leaving a note in the door that won't be visible (thanks to oxidation) for four hundred years.
Season 3
"And the Reunion of Evil". Stone manages to drive off Finkelstein in the ice cave and hold his own against Frost giants in a slew of games. Competing head to head with Jotun is something usually reserved for Gods and Epic heroes.
When he's subjected to a series of questions from the head Jotun, trying to figure out which is the real Finkelstein, Stone does enormously well just going off what he's observed and his knowledge of mythology.
In a combination of this trope and Heartwarming, Eve and the Librarians performing an intervention on Flynn to force him to remember that he's part of a team. It involves handcuffing him to a chair, tying his shoelaces together, and long lists of his faults.
In "And the Eternal Question", Ezekiel and Jake fighting off three vampires with their hands tied. Then nine more vampires rush onto the scene, they're surrounded and about to die...and Jenkins shows up and singlehandedly massacres all twelve with a pair of iron swords! Afterwards, he's not even breathing hard.
"And the Fatal Separation" has Flynn breaking himself and Stone out of a store cupboard with a bit of MacGyvering that would do the trope namer proud.
Stone showing off his martial arts proficiency by fighting off a series of ninjas. Even when he gets hit with a blowpipe dart, he still manages to fight off a few more before falling into the water.
It's also clear how much his fighting skills have improved in just a couple months; his strikes are much more precise, focused, and efficient. The choreography alone speaks to how much he's gotten better.
Later, he snatches three moving darts in midair.
The reveal that DOSA planted Eve in the Library as a sleeper agent, putting out the information about the artifact Flynn retrieved all the way back in episode 1 so that they would meet and recruit her.
In the "Wrath of Chaos" when the librarians turn Apep into a human so he can be sacrificed instead of Flynn.
DOSA confronts Jenkins, with Colonel Rockwell describes him as "ornery".
Jenkins: That's just for my friends. For you and your little back-up singers here, I'm willing to get downright nasty.
They then turn him to stone using Medusa's head, which is actually a testimony to just how dangerous they consider Jenkins. They have a large number of highly armed soldiers, and even they're afraid to Just Shoot Him, so they have to resort to turning him to stone.
And after the LITs release him and get him back to the Library, he damn near kills Eve in a fit of anger before she explains the Fake Defector bit that she and Flynn had cooked up. Not even a Guardian is a match for a truly angry Jenkins.
Jacob figuring out, with a bit of help from Ezekiel and Cassandra, the way to release Jenkins: There's no pictogram he can't solve, no math equation Cassandra can't figure out, no lock Ezekiel can't pick. So the answers have to be the exact opposite of what the Librarians would expect it to be.
Eve's whole plan, playing the General, the rest of DOSA, and a millennia-old Egyptian god like chumps with absolutely zero apparent effort.
The fact that Flynn has apparently had the longest tenure as a Librarian in the history of the Library.
