Final Crisis: Legion of 3 Worlds #5 (2009)

In the 31st Century, Superboy-Prime fights off the three heroic Legions and Superboy. At the end of time, the three founding Legionnaires and Superman battle the elder Superboy-Prime aka Time Trapper, who reveals that he became an anomaly that couldn't be killed after being shunted into the Multiverse, plus that he can access other alternate realities and intends to destroy the Legions in each of those realities. Superboy burns a scar on Superboy-Prime's chest, which also appears on the Time Trapper's chest. The original Saturn Girl and Brainiac 5 realize that time has become fluid, leading Brainiac 5 to deduce that the Time Trapper is a rogue sentient alternate timeline, and that his identity keeps changing with time. Back in Metropolis, Mordru uses the magics he absorbed from Kinetix to weaken the 3 Legions and empower the Legion of Super-Villains. He then launches an injurious attack on Blok, forcing the White Witch to invoke one of Mordru's dark spells against Mordru that absorbs his life force into her own. Mysa, now calling herself the Black Witch, uses her new magics to defeat the Legion of Super-Villains. Bouncing Boy and Duo Damsel, now calling herself Duplicate Damsel, then appear, where Luornu reveals that she gained the ability make multiple copies of herself after her second body was killed in the 21st century. At the end of time, the original founding Legionnaires use the Time Trapper's time portals to summon multiple Legions from across the Multiverse, who manage to knock the Trapper out. The founding Legionnaires and Superman then return to the 31st century with the Time Trapper. Superboy-Prime is repulsed by what he becomes, so he punches his future self, which erases both of them. The three Brainiacs reveal that the Time Trapper the Legion knew no longer exists as the future was reset when Superboy-Prime punched his elder self. After the battle is over, Sodam Yat recharges power rings on Oa to rebuild the Green Lantern Corps. The Black Witch travels to Zerox and claims Mordru's throne. The "Reboot" Legion, under the guidance of Shikari, decide to travel the Multiverse looking for other survivors, with Ferro naming the group the Wanderers. XS and Gates decide to stay behind and join the original Legion. The "Threeboot" Legion are revealed to be from a re-created Earth-Prime. Kid Flash and XS use Cosmic Treadmills to return the two Legions back to where they came from. Superman returns to the 21st century with Superboy and Kid Flash. Meanwhile, a powerless Superboy-Prime wakes up on the reborn Earth-Prime. He is reunited with his parents and his girlfriend Lori, who are all horrified by what he's become because they've read copies of the issues published by DC Comics from "Infinite Crisis" to "Legion of 3 Worlds". Superboy-Prime plots his return from his fearful parents' basement, remarking "They'll never get rid of me. I'll always survive."