In the manga, Shou, being a state alchemist, is killed by Scar. Nina is also killed.
In the anime, Shou was arrested and supposedly executed. (Nina was killed by Scar.) But really, the military kept him alive and put him in Laboratory 5 to work on creating the Philosopher's Stone. While in Lab 5, Shou made numerous attempts to bring back Nina as a human-looking chimera, and ended up turning himself into one. Shou later escapes from Lab 5 and ends up working with the homunculus and deadly sin Greed, and later betrays him and goes back to the military, working under the command of Frank Archer. Shou also betrays Archer and goes to work in an abandoned building to try and bring back his daughter. He succeeds, but the Nina he brings back is a soulless doll. Shou is last seen wandering back down into the depths of the abandoned building, muttering nonsense things and being delusional.