Back to the manga’s storyline, this is sort of incomplete since Keyhole messed up.
Temporary screenshots thanks to 2chan, expect tl;dr until they’re updated and it becomes less apparent.
Al and Gluttony arrive at father’s lair, and Al notices the resemblance between Father and Hohenhiem.
Ed, Lin, and Envy burst out of Gluttony, Al is happy to see Ed back. Father steps forward and Ed also notices the resemblance. When they mention this he’s surprised to learn that Hehenhiem is their father. He then heals Ed’s broken arm and repairs Al’s armour from with relative ease. Lin reacts by raising his blade.
Learning that he created the humonculi, Ed attacks him with alchemy but it’s easily blocked. Ed, Al, and Lin attack him but their attacks are all blocked as well. Father takes a step and does something that’s noticed even by those who aren’t in Father’s lair (such as Hohenhiem, Scar, and May). Ed and Al try to use alchemy but it doesn’t work.
They are then subdued by Envy and Gluttony. Father sees some use in Lin since the position of Greed is open. Ed draws the gun that Hawkeye gave him, Lin stops him since this was what he wanted. Father then drops the red philosophers stone into a cut.
Lin undergoes the transformation progress and it succeeds with Lin willingly accepting.
Scar and May Chang arrive, May reunites with Shao May and is disappointed when she see’s what Ed really looks like. Envy and Gluttony attack them, May’s rentanjutsu works. Ed tells Scar, that it was Envy that started the Ishval war, this causes him to attack in rage.
Ed confronts Lin/Greed, May recognises Lin, but not before Gluttony starts chasing her. Scar attacks Father but he survives and knocks him back. Al rescues May, and he and Scar retreat.
Al and Scar have something of a backs to back badasses moment when they surrounded on one side by Chimeras and Gluttony and Envy on the other side. Scar destroys a gas pipe and throws Al’s helmet while ‘destroying’ the water. this causes an explosion which kills Gluttony since he died too much. Envy grabs Al.
Ed and Lin/Greed exchange blows with Greed’s ultimate shield protecting Lin/Greed, Ed manages to knock him to the ground and reminds him of Lan Fan, hitting him at the same time this causes Lin’s personality to temporarily take over. Lin/Greed then restrains him, and Father tells Envy to return them to the surface. They leave knowing the Lin ‘is still in there’.
In the epilogue, Father extracts what is left of Gluttony’s philosophers stone and he fades away.
Ed, and Al return to the surface.
Temporary screenshots until I update them: