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troperville

The battle against multi-faced arm-sprouting huge anti-spiral ships. The opening mouths and eyes when the true strategy comes to surface (quite literally) will haunt viewers until the Grand Finale
Hearing Kamina's scream right after he was horribly mutilated by Thymilph's spear in Episode 8 can be pretty terrifying.
Still... Spinning...
The results of Simon's Heroic BSOD following Kamina's death. Seeing the cute boy turn into The Berserker who vanquishes Mooks with a No-Holds-Barred Beatdown, and is channeling so much Unstoppable Rage that his mech actually pukes and shuts down is... rather unsettling, to say the least.
Watching the Anti-Spiral disassemble Nia is terrifying. Her body is literally being pulled apart digital bit by bit, and she's disappearing as it happens.
- And It Gets Worse in Lagann-Hen. First, he disintegrates her bodysuit and then moves in on her with tentacles. Nia visibly struggles, and it's staged almost to make it look like he penetrated her.
The Anti-Spirals. A Hive Mind with god-like powers that has committed the near-omnicide of Spirals, their rap sheet includes: ripping off Majora's moon trick; having digital drones that can Zerg Rush you: inserting Messengers within every Spiral Race that don't even know of their true nature until the time is right and could be ANYONE, even one of your loved ones; being able to trap their enemies in alternate realities that can be their greatest dream or (presumable, even though it never happened in the series) their worst nightmare; and they have an avatar who looks like Slendy that has naughty tentacles and isn't afraid to use them. Oh, and the scariest thing about them? They think they're doing the right thing, even as they cross the Moral Event Horizon over and over and over again. The only thing that prevents them from being one of the most depraved people in all of fiction is that they are truly convinced that they're the good guys; even then, that may not be enough to redeem them. Why? Because instead of just taking the easy way out and using their god tier powers to Kill 'em All in one blow, they prefer to defeat their enemies by sending them over the Despair Event Horizon - and they enjoy it.