When Scott Summers was still a child, his father was flying his family to Canada when their ship was attacked by a Shi'ar spacecraft. Giving Scott the only parachute on board the plane, he threw his two sons out of the aircraft and into the Canadian wilderness. The two brothers were taken to an orphanage run by Sinister who later adopted the two of them, considering them the closest thing Sinister had found to genetic perfection. Scott quickly became Sinister's favorite of his two sons due to Scott's genes and ability to lead. This favoritism would strain the relationship between Scott and Alex, who grew jealous of his brother Scott. Unbeknownst to both Scott or Alex, their real father, Christopher, had managed to escape from the Shi'ar and made his way back to Earth in a Shi'ar airship. Unfortunately he was also infected with a Brood egg and his ship was captured by Apocalypse's forces. He was taken to the breeding pens where he was experimented on by Henry McCoy for a number of years. Cyclops began to question the treatment of the prisoners in the breeding pens and secretly began to release them. On one occasion, Jean Grey was captured by Cyclops during a mission with the X-Men and sent to Sinister's lab. However, Cyclops became attracted to her spirit and dedication to her past life. He contemplated returning Jean to her friends but Weapon X had infiltrated the labs and freed Jean himself, encountering Cyclops along the way. The two fought in a ferocious battle with Weapon X taking out Cyclops's left eye while Cyclops retaliated by obliterating Weapon X's left hand with an optic blast. Both Jean and Weapon X managed to escape but a bitter resentment remained between Cyclops and Weapon X.
After five years of being experimented on, Christopher Summers managed to escape from the breeding pens, much To Sinister's chagrin. He ordered his recapture but told Alex and Scott to remain behind, which made Scott suspicious of the nature of this mission. After the search team's emergency beacon was picked up, Cyclops and Havok went to investigate in the Ghost Lands where they encountered their long-lost father for the first time in years. Chris told them the story of how they became separated which was enough to convince Havok that he was telling the truth, but Cyclops wasn't as easily swayed to allow him back into his life so easily. During a battle between some scavengers, Sinister came and rescued the Summers family. Unfortunately, Christopher's Brood egg that was inside of him had hatched and he attacked Sinister. Before he could do any damage, Christopher's consciousness became dominant and he begged Scott to kill him, and Scott reluctantly complied. This act caused a further rift to appear in the relationship between Scott and Alex.
Cyclops soon learned that Apocalypse's Horseman, Death, was trying to cause a mutiny and seize power for himself. Cyclops knew he had to make a stand and helped Blink free her captured teammates and release Sunfire from his prisoner. Blink teleported Cyclops and then her teammates to safety as Sunfire incinerated Death. It was around this time that Sinister had created X-Man using both Scott and Jean as genetic templates, who were both unaware of this development. Sinister planned to use this mutant to overthrow Apocalypse as ruler. On one occasion, Cyclops came into contact with X-Man and tried to help him escape from the pens. However, the rash mutant refused his help and escaped the pens by himself. Both were unaware of their relationship to each other or that they were secretly been watched by Sinister himself. Cyclops also became increasingly concerned by Sinister's sudden disappearances. He broke into his lab and discovered the place had been thrashed. Cyclops realized that Sinister had abandoned them and betrayed Apocalypse.
Cyclops continued to rescue people from the breeding pens. Unfortunately people began to suspect that something was amiss. They questioned a young mutant named Lorna Dane who had witnessed the previous nights escape. Unfortunately, Lorna had a fragile mind and thought she had witnessed Magneto rescuing the prisoners. Alex ordered that she be interrogated by the Beast but Cyclops stopped the torture and ordered her release back to the pens. That night. Cyclops, in disguise, broke into the pens and rescued Lorna but his activities were detected by Northstar and Aurora. With his face hidden by the darkness, Cyclops attacked the two twins and made his getaway. Meeting a member of the underground at the Hudson River. Cyclops gave Lorna over to them. However, his face was no longer in disguise and his activities were been monitored by Havok from a distance. Jean Grey had returned to Sinister's lab in an attempt to locate him, but she was captured by Havok and sent to the Beast. Cyclops was stunned to see Jean again and when he refused Havok's order to kill her, Havok revealed that he knew Cyclops had been helping the prisoners escape from the pens. Cyclops was then captured and, along with Jean, was tortured by the Beast. However Jean used her psychic powers to remove Cyclops' visor and Scott released a concussive blast on the Beast, rendering him unconscious.
The two escaped and tried to free the prisoners in the breeding pens. However, Apocalypse had ordered that all of the prisoners be killed as a means to convey his message of survival of the fittest. Outside, Cyclops and Jean met X-Man who had come to dismantle Apocalypse's rule. X-Man discovered that the two were his parents while Jean and Scott both felt an odd connection with the boy. However, they wished each other luck in their journey and departed ways as Jean and Cyclops made their way to the Brain Trust. The Brain Trust psionically anesthetized the prisoners so they lacked the will to escape. Jean used her psychic powers to destroy the Brain Trust as Cyclops ordered the Bedlam Brothers, who had also betrayed Apocalypse rule, to disable the main generators and knock out all of the lights. As the prisoners escaped, Cyclops and Jean fought Havok with Cyclops knocking Havok unconscious. They both led the prisoners to safety but Jean sensed that the Human High Council had unleashed their bombs which were making their way to Apocalypse's America. In an attempt to hold the bombs back, Jean blanketed the sky with a telekinetic shield. Unfortunately Havok sneaked up from behind them and killed Jean and Cyclops with his powers. Weapon X avenged his beloved by stabbing Havok in the back and killing him.