Batman Grabs a Gun: During his battle with Bradley, Scar uses Alchemy to reconstruct matter for the first time, breaking his code as an Ishvalan in the process. Beforehand, he only used Alchemy to deconstruct matter and thus technically remain within the bounds of his code. Scar admits that after seeing the enormity of what's at stake, he relented and decided to accept Alchemy in order to go all out against the enemy.
Cosmic Horror Story: Escalates properly into one of these, ending with Father swallowing God.
Curb-Stomp Battle: Father versus the assembled sacrifices plus Mei and Greedling. It's fairly clear he's only indulging their efforts to hurt him, because as soon as the time for the transmutation comes, he ends the fight effortlessly.
Didn't See That Coming: Greed blitzing Father out of nowhere. A panicked Pride even lampshades it in-story ("Where'd he come from?!").
Downer Ending: Father succeeds in pulling off the nation-wide transmutation circle, meaning that everything our main protagonists have done to stop him have amounted to nothing. So there's little that can be done except witness as every character on this show has their souls forcibly taken.
Hope Spot: Greed comes out of nowhere to blitz Father and it seems for a moment that he might have actually killed him. Naturally, it's not that easy.
Eyecatch: May Chang and Shao May in the first, and Winry Rockbell in the second.
Villains Do The Dirty Work: Greed attempts to hijack Father's plot and interrupt the ritual (so he can steal the power for himself). Granted, Greed's more of an Anti-Hero at this point, and it doesn't work, but it's the thought that counts.
