Alternative Versions of Cyclops - Age of Apocalypse

In the Age of Apocalypse, Scott is a villain who fights against the X-Men. Just like in the normal timeline, Scott and his brother Alex were separated from their parents when their plane was attacked by a Shi'ar spaceship. The two would end up in an orphanage run by Sinister, though in this time line, both brothers were kept by him and raised as his foster children. Unbeknownst to them, their father Christopher Summers eventually makes his way back to earth, only to be found by Sinister and given over to the Beast (also a villain) for medical experimentation.

Both Alpha mutants, and both holding the rank of Prelate, Scott and Alex Summers dominate the new mutant aristocracy in Apocalypse's America. Sinister employs the brothers to operate his breeding pens, act as security, and sometimes perform as special ops unit. Scott's ability to show emotional restraint in battle earns him Sinister's favor over Alex, fueling a dangerous rivalry between the brothers. This rivalry worsens when the brothers reunite with their real father—Christopher Summers—but are forced to kill him.

Sinister's preference for Scott over Alex also spills over into his genetic experimentation, as with Scott's DNA Sinister plans to create a super-mutant strong enough to destroy Apocalypse. After capturing the X-Man Jean Grey, Sinister believes that he has found Scott's genetic match, and uses their combined DNA to produce a child, Nate Grey.

Despite an initial belief in the doctrine of mutant superiority and even being considered by Apocalypse as a candidate for Horseman, Scott has reservations about the ethics surrounding his work, primarily in terms of excess. These concerns grow substantially once he meets and becomes enthralled with Jean Grey, a prisoner and "race traitor." Though Scott plans to release her on his own time, Grey's lover, Weapon X, breaks in and liberates her himself. Scott fights back against Weapon X, severing Weapon X's hand, but losing an eye in the process. Jean escapes with Weapon X, who remains an enemy of Scott.

In the meantime, Scott increasingly finds himself questioning the treatment of prisoners, and secretly starts releasing them. This does not go unnoticed by his brother Alex, who still harbors hostility against him. Alex re-captures Jean in order to use her against Scott, successfully exposing his brother as a traitor. Although Jean has no love for either brother, she decides to trust Scott and they attempt to escape together. Along the way the two meet Nate Grey, their genetically engineered son, though they remain oblivious to the truth of their connection to him. Eventually, Alex tracks down Jean and Scott, he kills Jean and defeats his brother. In retribution for Jean's death, Weapon X kills Alex by revealing that while Scott blew off Logan's hand, his claws were retracted at the time. According to the records of Magneto, Cyclops was incarcerated for his crimes during the reign of Apocalypse.

When Weapon X became Weapon Omega, the Overlord, he had Cyclops killed and ressurrected by using the energies siphoned from the celestial life seed.