Ed 'dies' on the other side of the Gate and is revived in this world. Hohenheim is stuck there as his body has travelled to that side of the gate. Alchemy also doesn't work. He kills Envy in almost the same way Envy got him. Al, who used the P. Stone to save Ed, has dissappeared. Ed, seeing this, uses his own Alchemy to bring back Al who regains his 12 year old body. However, Ed ends up trapped on the other side of the gate in the process.
Mustang kills Pride using the Fuhrer's skull. Afterwards, he dissolves the position of Fuhrer and creates a cabinet to rule in its place. He and Hawkeye have a nice touching moment while Roy is in the hospital. Bradley did take out one of his eyes.
Dante gets eaten by Gluttony. Wrath survives and is given automail limbs to replace the ones he lost. It is assumed he lives a fairly peaceful life as the last we see of him is him sleeping in the woods near the Rockbell home.
Al is back as a human, but he can't remember anything that happened after they tried to revive their mother. The Rockbells and Izumi tell him the story and he is determined to learn alchemy in hopes of bring Ed back.
Ed, on the other hand, is now in 1921 Munich with his father. He studies technology, more specifically, the emerging field of rocket science, hoping to find a way home that way somehow.
The story ends with both brothers sitting on trains in different worlds, both vowing to find the other some way.