Unfortunately with the Naraku searching for him and opening a unique school during the Joui Wars, it seemed inevitable that he will be found.
It appeared that Shouyou succeeded in living a life without killing and death. Shouyou suppressed the other personalities, defected from Naraku, took in a child, and with their help opened a school to teach children. Thus he created another personality, Shouyou. The original personality watched in the background at his blood-thirsty personas and wanted to fight back and resist them. So he formed and lead the Naraku for 500 years, continuing to slaughter and kill yet along the way, developing a death wish.
He continued being a serial killer until he was caught by the imperial government, who instead of executing him, decided to make him into an assassin, seeing his potential. But at the same time, Utsuro's other personalities took over their shared body and decided to kill people, partially as revenge and partially to strive to become human again. He was then placed in prison and forgotten about for decades until he was able to leave when his cell door rotted away. To cope with the constant suffering and death, Utsuro created multiple personalities. Unfortunately he was persecuted by a wary populace who continuously tried to kill him to no avail, leading to them becoming more fearful and greater attempts to kill him, sparking a vicious cycle. Utsuro (original name unknown) was born with the ability to absorb and contain a high amount of Altana within his body, granting him near ageless immortality and high regenerative capabilities. They are still 16 and 14 respectively.Utsuro willing to let the Tendoshu analyze his body in order to get their help for his death.
But Shinpachi and Kagura are not grown up here. In other words, all relationships post-canon are established and everyone is whole and happy. So Shoyo/Utsuro and Takasugi are both alive.
Part 9 of Echoes from the depths of Gintama Rare Pair Hell
Except it's not exactly happy, because things are complicated.) Series (One of those AUs where Oboro is a senior student at Shoka Sonjuku. Instead of abandoning Oboro for dead, Shouyou digs Oboro out from under the rocks.