Giovanni: Eloped with his childhood friend Angelo (aka Lyra’s dad) to Unova after being defeated by Red. The two own a restaurant together there and also use the space as a neutral meeting ground for the Castelia Mob. Jessie and James (and their son Jules and daughters Jill and Josie) work there, later joined by Renato when he runs away from home. Giovanni is on good terms with both his kids (on better terms with Silver though) and spoils his grandkids rotten.
Maxie & Archie: While helping to clean up after Archie’s mess of summoning Kyogre, Maxie ends up the guardian of a girl, named Kiran who was orphaned when her parents drowned in the raging storms. While he might not seem like a fatherly figure, he ends up stepping up to the occasion quite well. Eventually, after receiving funding from Aether Foundation, the former Team Aqua and Magma merge into one group, which is also around the time their leaders start to acknowledge their feelings for each other. On paper, they got married for tax benefits and to make things easier for Kiran. In practice, they are totally in love. The two are retired now, but oversee their old teams nonetheless (and dote on their two grandchildren.)
Cyrus: He remains in the distortion world until his niece Dawn comes to find and convince him to give humanity another shot. He ends up moving in with his older sister Johanna and her family in Twinleaf and now lives a quiet and relatively happy life. He was somewhat surprised to find that the (in his mind) very irrational one-night-stand he indulged in with Jupiter towards the end of their plans resulted in a son. He has some regrets that Callisto grew up with a rough life, but is pleased that he seems to have become a well adjusted adult, even marrying the daughter of one of Cyrus’ other former commanders. Cyrus also is quite fond of their daughter – his granddaughter – Pina.
Ghetsis: When he threatens Rosa’s life at the end of the BW2 plotline, Rosa’s Hydreigon partner, Cassandra, mauls him to death. Nobody particularly mourns his passing, though Rosa ends up very shaken by being indirectly responsible for someone’s death, no matter how horrible a person they were.
Lysandre: He dies when his secret base collapses, leaving behind two unborn sons from different mothers.
Lusamine (Note, this AU follows the USUM plotline): Realizing that she was far from an ideal mother, Lusamine decides to let her children go their own way and no longer interfere in their lives. She dedicates her life to research, currently trying to find ways for Fallers to regain their memories, or to prevent the memory loss in the first place.
Guzma: With Team Skull no longer really being a thing and having helped save the world, Guzma finds both himself and those around him more willing to reach out and try to form bonds. A number of his old friends and rivals from his days as a trial goer get back in touch with him, including Kukui and Molayne. After hours spent hanging around the observatory, Guzma and Molayne eventually develop feelings for each other, especially after Molayne suddenly ends up the guardian of his niece and Guzma helps out immensely with taking care of Vriesea Currently, Guzma is ‘technically unemployed’ but really he just helps out people with any odd jobs they need, and of course he always supports his Best Niece Vriesea in her endeavors to form ‘Team Skull 2′.