At the end of your second faction mission for The Illuminati (You have to go to Shambala to retrieve an artifact of great power from a turncoat Templar) The Pyramidion reminds you he is not to be fucked with:
In the Dragon edition of the same mission, your contact casually mentions that they not only arranged the rogue agent's defection, but his career, his upbringing, his conception- even the fact that his parents met at all; the only reason why this guy was ever born was because the Dragon needed someone in the Templars to go renegade!
The into to "Revenge Best Served Hot." Bearing in mind that these next few lines come from two traumatized teenagers with no combat experience whatsoever, it becomes all the more awesome.
Aurelie: Werewolves, they are not an endangered species, are they?
Next mission intro, Celine is hacking incoming werewolves to bloody shreds, while Aurelie snipes the remaining few with a rifle- at one point casually nailing one of the sneakier ones right between the eyes. Once again, these aren't trained soldiers; they're stranded backpackers with no experience in combat or even the most basic knowledge of the secret world.
Aurelie: You know what they say about wolves and pretty young girls.
Celine, surrounded by five dead werewolves and unable to hear over her chainsaw: What?!
Carter finally getting the chance to cut loose with her powers in "Carter Unleashed." Watching familiars vanish in massive firestorms is impressive enough; the fact that this is an Escort Mission where the supposed damsel in distress is powerful enough to clear an entire room with one blast of magic just takes it to awesome new levels.
Montag admitting that he has firsthand knowledge of how to subdue a rampaging familiar- proving that he's Headmaster of Innsmouth for a damn good reason.
"A teacher is only as good as his tools!"
The intro to "From Carthage To Cairo." After being told that her deals with the Atenists will no longer be tolerated, Tanis pulls a gun on Säid. The mummy responds to this by sniffing the barrel and remarking that he smells gun oil, cheap perfume and desperation- before casually pushing the gun aside. For good measure, this actually pushes Tanis into frantically making counter-offers with all the wealth of the Phoenicians. Säid is not impressed.
In "The Prisoner," you're captured by the Atenists and your powers are temporarily disabled... thus giving you a chance to fight your way out bare-fisted!
Also in this level, the final beatdown you deliver to Saddur: after slugging him in the chops, kneeing him in the stomach, and headbutting him in the face, you kick him hard enough to impale him on a nearby pole!
The very end of "Last Train to Cairo." Epic duels atop a moving train. 'Nuff said.
The end of the Egyptian mission, 'Black Sand, Red Sun', results in that 'prophet' of Akhenaten, Abdel Daoud, summoning endless waves of followers to prevent you from getting into the Black Pyramid properly. Then in come the NPCs you've been helping throughout Egypt, and the Marya and Orochi fight the villains to a standstill, opening up the way for you to get through.
Lilith's introduction. Rarely have villain introductions been so gloriously hammy. For good measure, she actually manages to one-up Beaumont's clever tendencies by sawing your legs off!
Arturo Castiglione making his stand against The Phoenicians who are blackmailing him to stall the faction agents from entering Tokyo.
Arturo: "I will not lay down anymore. I will defy the Phoenicians and all the looming powers!" *Answers phone* "What do you want? No. I will hold them back no longer. They are coming for you. They are ready. The time you imposed has sharpened the knives that will be at your throat. You have no more power over me. In vinculis etiam audax."
While Sonnac and the Templars certainly have nothing but disdain for Orochi and Bong Cha and the Dragon seems to be more annoyed at them than anything else, KG positively steals the show in summing up the relationship between the Illuminati and Orochi.
The Jingu Clan, the House-In-Exile and the Korinto-Kai launching an all-out attack on the tower, complete with scenes of Jingu samurai duking it out with Orochi drones, Oni casually teleporting themselves over landmines, and a few of your allies taking Kiyota's advice and moonwalking across pressure plates! For good measure, just when it looks as though the attack is going to end in a massive brawl between the Jingu and the House-In-Exile, Daimon Kiyota steps in to forge an awkward truce between them - all for the sake of bringing down Orochi, of course.
Samuel Chandra finally unveils himself, complete with some eerily chilling monologues. For good measure, he also unveils his secret weapon: an entire squad of Bee-empowered operatives loyal to Orochi, complete with portable Anima wells. Some of the most entertainingly challenging boss battles in the Issue ensue.
The Mitsubachi are standing between you and the penthouse elevator, and this time you can't trap them out of reach: for a while, you're at an impasse and unable to tip the odds in your favour... and then all three major factions in Kaidan pull a Big Damn Heroes moment, with Daimon Kiyota in the lead with Guns Akimbo!
John finally overcomes his fear of Lilith and attacks her with all the bodies at his disposal.
I am the pirate signal. Let me in. I am the word virus. Let me in. I am the ear worm. Let me in. I am the brain pathogen grammar. I am the Dreamers' dream. I am what I am. Let me in. Let me in. Let me in. Let me in. LET ME IN.
The final reveal at the Penthouse: it turns out that John's been manipulating you all along, all for the sake of finishing the mission he failed when he was still human: removing Lilith as a threat. Better still, it works. His distractions succeed in keeping Lilith preoccupied long enough for the Nephilim to sweep in and carry her off. As a final cherry on the victory sundae, a Black Lore piece on the balcony revealed that this mission was the only thing keeping him from leaving Kaidan, and now that you've helped him complete his Unfinished Business, he's free to plague the world at his leisure.
Daimon Kiyota has one at the very end, revealed only to Dragon players: there's been a dramatic change in management at Dragon headquarters, with the Child maturing into a teenager, Bong Cha being fired, and Daimon Kiyota now running the show as the new Voice of the Dragon - just as he always wanted. For good measure, both the Illuminati Talking Heads and the Templar Old Guard furiously observe that Kiyota and the Dragon are the only faction that got what they wanted in Kaidan.
Samuel Chandra making good on his threat against you, if you bring harm to Lilith, by using QBL's massive media resources to frame members of all factions for the Tokyo bombing.
An off-screen moment for King Solomon, a human who managed to trick the Unbound into being imprisoned. The entity in question was considered uncontrollable by both the Host and the Dreamers but Solomon managed to pull it off.
Another is that he is the reveal in Lore that King Solomon is one of the few beings about which even the Buzzing knows hardly anything. They can tell you about the 1st Age, about demons and angels and beings that could easily wipe Earth from existence, but the only way they can track King Solomon is whenever he does something big enough to draw large amounts of attention.
The player character's encounter with the same spoilered being counts as well, giving you a chance to defeat said entity in its prison.