So in Season 2 Flynn blurted to Moriarty that he loves Eve, and then he and Eve do the True Love's Kiss thing, but I don't think we actually hear Flynn say "I love you" until halfway through Season 3, and the fact that the airport scene was a whole big deal made me think that maybe "I love you" was kind of an unspoken assumption until that moment. I took that idea and ran with it.
Title from "Tear Up This Town" by Keane
Watching Eve whirl through their attackers, Flynn honestly begins to wonder how he survived for so long without a Guardian. She leaves three men unconscious in her wake in the time it takes him to subdue one. The cult leader's monologue ends when she delivers a vicious punch to his head, and then she yanks the ancient pendant from around his neck; the remaining adversaries drop immediately to the ground. She tears a strip of fabric from the leader's shirt and uses it to wrap up the artifact, then jokingly presents the bundle to Flynn like it's an expensive birthday gift.
"Oh, Eve," he plays along, brushing their hands together as he takes the artifact, "I love y—it." His eyes go wide, but she doesn't seem to notice what he almost said.
(He distracts her with a kiss, just to be sure.)
(As it turns out, kissing her distracts him, too.)
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For all his degrees, Flynn doesn't claim to understand love. He's always believed that "I love you" should be reserved for candlelit dinners, picturesque sunsets—things of high romantic calibre. So he doesn't understand why half the things Eve does have him biting back those words: when she smiles at him between bites of reheated pizza, or when she treats ancient texts with the same amount of respect as he does, even though she has no clue what they say; when she doesn't get mad at him for using the Back Door to stumble into her apartment at three in the morning, and when she does get mad at him because he tried to go after a demon-summoning artifact on his own. She bails Ezekiel out of a Russian jail and drags him back to the Annex by his ear, and Flynn nearly says it between bursts of laughter.
He frees her from a spell with True Love's Kiss and he still doesn't say it (Stone eventually finds out about that and calls him a "giant freaking idiot"). He doesn't understand why he can't open his mouth and let the words roll off his tongue.
(He sees two women exchange casual "I love you's" after a parting kiss outside of a bookstore in Milwaukee, and he briefly considers following one of them and asking her how they got to that point in their relationship.)
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He finally says it in a crowded airport while the team sneaks a definitely suspicious object through security. He's never imagined it would be like this, almost whispering it at the tail end of a distracting/metaphor/argument, and the dip-kiss is probably a little over the top, but he's always been better at using his actions and desperately needs to her to know that he means it.
(He doesn't make a habit of saying it in front of the other Librarians, but he's never had the best brain-to-mouth filter.
"Love you," he says when she briefly catches his hand before she leaves on a mission with Ezekiel.
Cassandra doesn't quite manage to muffle her excited squeal, and Flynn realizes that it's the first time he's said it in public since Venezuela. Jenkins and Stone are both trying to look impassive, but Jenkins allows himself a small smile and Stone ends up outright hiding his grin in a book. Even Ezekiel, waiting impatiently by the door, doesn't make a comment.
Eve smiles and gives him a quick kiss, repeating his words in a whisper against his lips.)
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"Did you really not know?" he asks softly once they're back in her apartment.
"I think I've known for a while" she says, taking his hand as she sits next to him on her couch. "True Love's Kiss and all. It's just better to actually hear it."
Flynn looks at his lap and ponders this new information, but then Eve grasps his jaw and forces him to make eye contact and says, "I love you, Flynn," and oh, it makes sense now.
There's no sunset, no candles, just the dim glow from a lamp and moonlight peeking through the curtains, and he realizes that he prefers this moment to every moment he's imagined.
"I love you," he says easily. There's a goofy smile on his face because he can't figure out how to make any other expression right now, but it's okay because she's smiling back at him, and he thinks that all the magic in the Library can't make him happier than he is now.