In the months following Stryfe's master plan, the X-Men and allies could only wonder if Cable and Stryfe had indeed perished in the explosion. Their questions were answered when Cable returned from his time era, explaining that he had appeared there following the explosion, a feat which Stryfe had not managed to duplicate. Unknown to Cable, however, was that while Stryfe's body had indeed been destroyed, Stryfe's mind survived as a secondary consciousness within Cable's own.
Shortly after returning, Cable was visiting the grave of Madelyne Pryor when he was confronted by Mister Sinister. Possibly motivated by Stryfe's reneging on their deal, Sinister provided Cable with all the answers he had been searching for regarding his origin and identity. When all parties involved in the X-Cutioner's Song conflict learned of the lineage of Stryfe, they were taking Stryfe's word for granted. However, Sinister now revealed to Cable that they were all misinformed. The true son of Scott Summers and Madelyne Pryor was Cable. Stryfe was but a clone and not vice versa like they had believed. Sinister further revealed to Cable that the arms dealer Tolliver, who had given Cable so much trouble over the past several months, was none of other than Cable's adopted son, Tyler. Before leaving, Sinister created further turmoil by causing Stryfe's personality to emerge and gain dominance over Cable's body.
The Askani Sisterhood sent back a second operative to warn Jean and Scott of the reappearance of Stryfe, 
but the woman was intercepted by Tyler and Zero, which Tyler had "inherited" after Stryfe's apparent demise. Using his empathic powers on Askani, Tyler tried to find out the truth about Cable and Stryfe. From visually displaying her memories, Tyler and Stryfe, who had tracked down the energy signature of the time-traveler, learned that it was Stryfe who was the clone and not Cable. The knowledge was too much for Stryfe to handle and he refused to believe it, starting a fight with Tyler. Zero ultimately realized that they would cause unwanted destruction, so he teleported in Xavier, Cyclops, Jean and Domino. Together, they convinced Stryfe into letting go and, with his consciousness expunged, Cable was himself again. In the confusion, Tyler escaped. [Cable (1st series) #6-8]
The manner in which Stryfe's consciousness departed is not exactly clear, however it seems that at some point the consciousness, or "soul," somehow came into the possession of the demonic entity known as Blackheart, the son of Mephisto. For some time, Blackheart enjoyed tormenting his latest possession, but like all collectors looked ever for an opportunity to trade for something more valuable. The opportunity arrived when the X-Forcer Warpath was killed by a mutate, providing Blackheart an opportunity to strike a deal with Stryfe. Blackheart would temporarily divert Warpath's soul to his infernal realm and, if Stryfe could crush Warpath's spirit and thus bind him to his Hell, Blackheart would allow Warpath to take Stryfe's place. Stryfe would be returned to life in the Apache's body to sow chaos as he saw fit.
Luckily for Warpath, one of his teammates was Danielle Moonstar, who still maintained a spiritual connection with the Valkyrie. One of these warrior maidens, Brunnhilde, arrived to Moonstar and warned her of what had occurred to her teammate and offered assistance in transporting them to the demon's domain to save him. Along with her teammates Sunspot and Boomer, Moonstar arrived to find Stryfe still at work on Warpath. 
Despite Stryfe's best attempts, Warpath remained strong in spirit and Stryfe's window of opportunity in his bargain with Blackheart was at an end. The arrival of Warpath's teammates tipped the scales and Stryfe was again cast into a demon-filled lake of fire by Blackheart, who gloated that the whole purpose of the exercise was to give Stryfe false hope, making his suffering all the more meaningful. Their task complete, the X-Forcers (Warpath included) returned to the living. [X-Force (1st series) #73-74]
Damned, as he seemed to be, for all of eternity in Blackheart's realm, Stryfe inexplicably once again plagued the land of the living, with no explanation as to how he had returned. Possessing a pyramid-like shaped "Pyramond" that he launched from the Earth's moon, Stryfe landed his flying fortress onto Castle Doom in Doomstadt, Latveria. At first, the capital's populace wondered if it was the return of their lord and master Doctor Doom, who had disappeared since the incident with Onslaught in New York, but soon learned differently when Stryfe, flanked by his Dark Riders, emerged from the Pyramond.
The first orders Stryfe bestowed upon his followers were to kill all of the world's remaining telepaths, which Stryfe declared the greatest threat to his rightful reign. Fortunately for Stryfe, at this time all of the world's telepaths had lost their abilities due to the recent Psi-War. This was equally unfortunate for Nate Grey, who was visiting Doomstadt at the time and only had his telekinesis to protect himself and the recently-resurrected Madelyne Pryor against the Riders. 
As Madelyne teleported away for help, Nate found himself attacked by the mental manipulating Rider called Psynapse, the accidental result of which was the restoration of Nate's telepathy.
Rather than being displeased, Stryfe was at first merely intrigued by the youth's power but then mesmerized once he telepathically grasped all that was Nate Grey. Just as Stryfe himself was a warped mirror of Cable, Stryfe realized that Nate something similar, albeit from an alternate reality and possessing powers rivaling or surpassing his own. Immediately, Stryfe captured Nate and took him into the Pyramond, intending to siphon the youth's immense psi-energies into himself. At this crucial moment arrived Cable, who had been found by Madelyne and brought back to Latveria to help. Unfortunately, he was too late and Stryfe used his increased abilities to defeat Cable and psychically convert Madelyne to his side. Almost powerless, Cable and Nate fled but soon returned for a rematch. Once again, Stryfe seemed assured of victory, but the timely intervention of an ally named Ness provided Nate the distraction to turn Doom's power siphon back onto Stryfe. The resulting energy-feedback loop caused an explosion which destroyed the entire Pyramond and, presumably, Stryfe with it. [X-Man #45-47, Cable (1st series) #63]
Despite his latest appearance of death, Stryfe yet lived. He soon came across the remains of Bastion's Prime Sentinel program, which had transformed humans into human-Sentinel hybrids capable of activation at a remotely sent signal. From the hidden base in Belize, Stryfe sent an activation code via e-mail to previous agents, one of which was Lady Deathstrike. However, Deathstrike had previously purged herself of all such programming for this very possibility. 
When Stryfe then sent successfully activated Prime Sentinels to destroy her to cover his tracks, Lady Deathstrike sought the aid of the X-Men.
The X-Men destroyed the four Sentinels and tracked their origin back to Belize, where the trail eventually led them to Bastion's old base and to Stryfe himself. Cocky as ever, Stryfe was more than a match for the most of the X-Men but found he had a literal blindspot when it came to Psylocke. Too reliant on his telepathy over his other senses, Stryfe found the mentally-shielded Psylocke telepathically invisible and thus able to strike a critical blow against him. With Stryfe's nervous system shredded by her psychic sword, Wolverine and Rogue were freed and able to fight back. Wounded and outnumbered, Stryfe chose to abandon his latest plan and to teleport to safety. [X-Men Annual 2000]
Whether it was because of Psylocke's attack on his nervous system or his time in Blackheart's realm had finally caught up to him, the next time Stryfe made his presence known he was a changed man. No longer a man of confidence or any trait that could be recognized as having belong to the one called "the Chaos Bringer," Stryfe had succumbed to paranoia, convinced that he was being hunted by Cable, who was beset on killing him. Panicked for aid, he entreated the aid of the mysterious man called the Witness, who in turn recruited a dubious Gambit and Bishop. Incredulous at being asked to guard a mass murderer, Gambit and Bishop immediately refused, though they soon questioned their resolve when Cable arrived, all too prepared to kill the cowering Stryfe in cold blood.
Before Cable finished the job, however, Stryfe admitted to knowing of the malady recently affecting Bishop. Having returned from a trip through the timestream, Bishop's unique energy absorbing abilities had inadvertently served as the host body of Le Bete Noir, an impossibly ancient entity which the Phoenix Force had trapped within the Earth's core five billion years before. Still sheepish in his demeanor, Stryfe apologized for his intention to use Le Bete Noir to destroy the world, a failing he blamed on his innate nature. 
As the X-Men reeled, flabbergasted at the stunning admission of guilt, Le Bete Noir began to arise from Bishop. As the only thing stopping its reign of destruction was Stryfe's telekinesis, Bishop pleaded to be killed to stop it. However, Stryfe offered another option and absorbed Le Bete Noir himself. As his body was consumed by the ancient entity, denying it a foothold on Earth, Stryfe apologized to Cable for all of his sins. Before the group's eyes, Stryfe discorporated into ash. [Gambit & Bishop #2-6]
Somewhere along his personal timeline in the near future, the inexplicably still living Stryfe was visited by Bishop during a critical moment in Bishop's life. Ever the loyal X-Man, Bishop had suddenly betrayed his teammates when he tried to kill a newborn baby, which Bishop was convinced would grow up to perpetrate the crime for which mutants in his native timeline had been persecuted. Believing her to be a messiah instead, Cable accepted custody of the young girl whom he eventually named Hope and time-traveled into the future to raise her in safety. Intent on hunting them through time, Bishop's only advantage over Cable was that Cable could only travel forward in time. To even the odds, Bishop limited the pair's hiding places by rendering uninhabitable every continent in the world except North America.
Along the way, Bishop came across the slumbering form of Apocalypse, oblivious and helpless to the outside world while in his regenerative phase. Realizing that this could be the perfect incentive for an ally to set his trap, Bishop traveled back in time and offered a deal to Stryfe: help him kill Cable and he would give Stryfe Apocalypse. Though he no longer harbored animosity toward his genetic template, Stryfe eagerly accepted the bargain and traveled into the future where the two confronted and killed Apocalypse. Stryfe then went about conquering the last habitable continent of North America and built a gleaming city from which he could administer his empire and await the arrival of Cable.
Eventually, some years later in the late 30th century, Cable and Hope arrived as expected. Unexpectedly, so too did Cyclops' clandestine wetworks group, the latest incarnation of X-Force. Having successfully pinpointed Cable and Hope in the future, the team was sent into the future to retrieve the two of them and kill their pursuer, Bishop. The two groups' arrival did not go undetected however and, after a cadre of his troops failed to capture them, Stryfe arrived in person and captured Warpath and the young Hope. 
Taking his prisoners back to his throne room, Stryfe was at first dismissive of the young girl until Bishop attempted to kill her, causing Stryfe to wonder who she might possibly be. Before he could divine answers, however, the rest of X-Force and Cable arrived, attacking with lethal force. As in the past, Stryfe proved too powerful for his adversaries and easily defeated X-Force.
At the cusp of victory, however, Stryfe learned to his horror that Apocalypse yet lived. Found by Archangel, who had recently resumed the mantle of the Horseman Death and had been drawn to Apocalypse's location, Archangel restored his former master, who now brought vengeance upon Stryfe, proving which of the two of them was truly the weak. Under the fists of Apocalypse, the age of Stryfe came to an end. Worse yet for Stryfe, it seemed that Apocalypse intended to use him as he had when Stryfe was a child, so long ago and so far in the future: as a host vessel. Whether Apocalypse succeeded in accomplishing what was previously deemed impossible, or what might happen to Stryfe upon learning it was not, is yet to be seen. [Messiah War crossover]
