Sephiroth leaving Shinra and joining Avalanche because he thinks it’s the right thing to do, but they kinda end up using him too much because they believe he needs to “make up” for all he did under Shinra, but then they slowly realize he is extremely tired and depressed. He starts breaking down, trying to do his best, but nobody has ever just let him rest or live normally. He can’t escape only being valued for his inhuman traits, never his soul as a person.
Sephiroth standing around Avalanche HQ with the world's deadest thousand yard stare, slowly realizing he's just traded one prison for another, realizing that the cycle of war and violence will just continue to the end of time and he will ALWAYS be forced into the heart of it against his will.
He grows inconsolably depressed, to the point where he begins to detach himself from reality, fighting without expression or interest in his surroundings. He's just so tired. And you can tell the world has slowly broken him. Despite everything, despite freeing himself from Shinra's abuse, he's still alone. If not more alone than ever.
Eventually, Team Glenn finds him during a collaborative mission. Whereupon Sephiroth finally breaks down and, at first, lashes out at them for leaving him, unloading all the bitterness and bile he's felt in his heart for years and years. Before crumbling at Glenn's feet, beginning him to tell him that he's not a cyborg, asking why he was born, asking him if he can just end it. And join Rosen.
Glenn takes charge and has Sephiroth medically discharged, threatening to pull his men out of the organization if anyone tries to drag Sephiroth out into another battle. He and the others find Sephiroth a nice, quiet place to live away from the fighting. And spend a long time with him there nursing him back to health. Eventually, however, the war with Shinra grows dire and Glenn knows they have to leave again. And, inevitably, leave Sephiroth behind once more. Sephiroth says nothing when he tells him. He just grabs Glenn's arm and spends an entire minute refusing to let go, before eventually giving up and slackening his hold. Glenn promises that they WILL come back once things calm down. Sephiroth... doesn't respond at all.
He spends most of his time in solitude, sleeping and not moving around all that much. And when Shinra inevitably finds him again on one of their hunts, he doesn't really react, finding it all too predictable but lacking the will to live to fight them. Or fight FOR them.
He is dragged off to be euthanized after several fruitless attempts to "rehabilitate" him. What becomes of him thereafter is unknown. Some say that Genesis broke in and saved him at the last minute. Others say several traitorous soldiers (Cloud and Zack) snuck him out. Some say that he died willingly and peacefully, his long life of suffering finally, finally over. You'll just have to fill in the holes yourself 😈
