Subverted with Father. He initially appears to be this, but soon reveals his true colors as Faux Affably Evil.
Amnesiac Dissonance: The newly-born Greed has none of the memories of the previous incarnation (including originally meeting the Elrics in Dublith), and is loyal and obedient to Father.
Badass in Distress: Ed, Al, and Ling already weren't doing well in their fight against Father, but after the latter nullifies the Elrics' alchemy, all three of them are promptly captured and restrained, giving Father the chance to inject Ling with a Philosopher's Stone.
Bait the Dog: Father initially seems friendly enough—seeming delighted when he finds out that Ed and Al are Hohenheim's children, healing Ed's wounds and regenerating Al's missing hand, and chiding them to take better care of themselves. And then he casually orders Gluttony to devour Ling, and when Ed and Al plead with him not to, he coldly and callously replies that Ling is completely useless to him.
Battle in the Center of the Mind: Subverted with Ling, after Father injects him with the Philosopher's Stone. Ling is attacked by several of the souls in the Stone, but when Greed appears (and seems to fully expect to have to do this with Ling in order to gain control of his body), Ling willingly gives up his body and allows Greed to possess him, in order to obtain the immortality he's been searching for.
Brought Down to Normal: Father "shuts off" the Elric brothers' alchemy, which renders them powerless long enough for Envy to restrain them.
Cassandra Truth: Subverted. Ed tells Scar what Envy confessed to him and Ling in Episode 24 about the Homunculi being behind Ishval. Scar takes a few moments to process this, but believes Ed and 'asks' for details from Father and company. A justified example, as Scar has encountered the Homunculi in earlier episodes and knows there's been something deeper going on here. Likewise, Scar's encountered Ed enough times by now to know the pint-sized Amestrian is many things...but he's not a liar.
Character Death: Played with with Gluttony. He does sort-of die as he uses up his Philosopher's Stone and has to be reabsorbed by Father (and disappears from the story for a while), but it's explicitly established that the "death" is not permanent, and that Father will re-create Gluttony later (with all of his memories intact, unlike Greed, so he'll still be the same person).
Chronic Hero Syndrome: In typical Elric fashion of wanting to save everyone they can. Despite May having previously been an enemy to the Elrics, Alphonse still saves her from Gluttony after she is injured and then tries to escape the sewers with her in order to protect her from being killed by the Homunculi.
Darkest Hour: Certainly one of them (combined with events from the next episode): the Elric brothers learn some terrible truths about their country, are rendered incapable of defending themselves when Father "turns off" their alchemy, and are captured by the Homunculi; their close friend Ling is turned into a Homunculus when he is possessed by Greed, with Ed and Al powerless to save him; and May is badly injured by Gluttony and has to be carried to safety by Al.
Enemy Mine: Downplayed example. While the Elrics, Scar, and May all arrive at Father's sanctum more or less simultaneously and clash with the gathered Homunculi, they're not explicitly teaming up during the fight. Al and Scar briefly collaborate towards the end, but that's really more so to protect May and get her out of there.
Fist Bump: Ed and Ling after realizing they've escaped Gluttony's stomach.
Get a Hold of Yourself, Man!: When Ed is fighting Greed and trying to get through to Ling, he punches Greed in the face while reminding Ling that he has a country and a friend (Lan Fan) waiting for him to come back.
A God Am I: Father's attitude. When Ling accuses him of looking down on humanity, Father contemptuously replies that he considers humanity so far beneath him that he can't even bother to consider them fools or care about them at all.
I Lied: Envy's response when Ed reminds him that he promised to tell him everything once they escaped Gluttony's stomach.
Lack of Empathy: Envy as usual, but Father is shown to have this as well. He offhandedly orders Gluttony to devour Ling, whom he considers to be a useless extra, and when Ed and Al plead with him to spare Ling on the grounds of him being their friend, Father coldly replies that he doesn't care, and Ling being their friend doesn't make him any less useless.
Nice Job Fixing It, Villain: Envy's gleeful confession about the Homunculi's role in Ishval during Episode 25 ends up biting the Homunculi in the ass hard here. During the fight in Father's chambers, Ed shares the intel with Scar (who believes Ed and is, to say the least, pissed). Discovering the truth has a massive impact on Scar's character development from hereon out.
"Ray of Hope" Ending: While the ending is ratherdismal, Ed and Al have one hopeful thing to hold on to that's gone right: Ling's consciousness is still alive inside the new Greed, as evidenced when he reacted to Ed's mention of Lan Fan.
Red Herring: Until now, Father's extremely close resemblance to Hohenheim made it look like they were the same person, and that Hohenheim was the evil mastermind behind the Homunculi. The Elric brothers even mistake Father for their dad when they first see him. However, this episode reveals that Father is not Hohenheim, though he clearly does know him.
The Stinger: Since Gluttony has used up too much of his Philosopher's Stone and is on the verge of dying, Father reabsorbs him for the time being, promising to rebirth him soon with all of his memories intact.
That Man Is Dead: Greed insists that Ling is gone, and he is the only one left. Ed, however, manages to prove that this isn't true, and Ling's consciousness is still present inside Greed.
May's fury at Shao May being "kidnapped" leads her to lash out at everyone else present with her alkahestry.
When Ed reveals to Scar that Envy was the one truly responsible for the shooting incident of the Ishvalan child that ignited the Ishvalan Civil War, Scar does not hold back in fighting the rest of the Homunculi.
Use Your Head: A variation—Scar throws Al's head at the attacking beasts.
Villain Respect: Greed towards Ling to a certain degree, as he—a being who, by nature, wants everything he can get—is quite impressed by Ling's own avarice and ambition.
Wham Shot: Scar is still able to use his Right Arm to attack Gluttony despite Father having shut down all Amestrian Alchemy minutes earlier. The Homunculi are left flabbergasted.
