General Philip Rey first came to prominence while fighting the forces of the Cobra splinter group, The Coil, in Europe. When he came face-to-face with Major Bludd they fought with knives, and the fight ended with Rey cutting off Bludd's hand. Shortly after, he was recalled to Washington, DC to meet with the cabal of generals known as the Jugglers. The G.I. Joe team's commander, Hawk, had recently been shot and paralyzed during a battle with Cobra. The Jugglers decided to crack down on the team after having several Joes arrested and cutting the team down to a twelve-member roster. They then gave Rey command of the team. Some Joes were suspicious of Rey when he took command, and wondered why they had heard so little about Rey's career until recently, and why much of the information about his past was classified. Over a year later, their suspicions proved well founded when the truth about General Rey was finally revealed.

    General Rey's true origins began many years earlier, when the Cobra scientist Dr. Mindbender used advanced cloning technology to combine the DNA of history's greatest military leaders and conquerors to create a super-soldier to fight for Cobra. The result was Serpentor, the Cobra Emperor. During his work to create Serpentor, the Doctor created eleven other clones who had not been artificially aged as Serpentor was. Cobra Commander ordered them destroyed, but in reality Mindbender kept the clones hidden away in a secret laboratory on Cobra Island that was unknown even to the Commander. Mindbender secretly experimented with one of these clones, aging it and altering its appearance. With the help of the hypnotist, Crystal Ball, the clone was programmed to be suggestive to commands and controllable through various post-hypnotic code-word triggers. Mindbender hoped to use the clone as a secret weapon against both G.I. Joe and Cobra, should the need arise. Mindbender recruited Zandar to use a false identity to set up a sale of the clone to at least one of the Jugglers. They were unaware of the post-hypnotic suggestions, allowing Mindbender to have a sleeper agent hidden amongst his enemies. Serpentor was killed during the war between his forces, allied with G.I. Joe, and the army of the Cobra Commander imposter, Crimson Guardsman Fred VII. Some time later, Dr. Mindbender, too was killed upon the return of the true Cobra Commander and was unable to continue his plans. After an international military force defeated Cobra and scattering its members, the United States Army seized Cobra Island and took the remaining clones into custody.

    During the years without G.I. Joe and Cobra, a group loyal to Serpentor known as The Coil had carried on Mindbender's work and created a thirteenth clone, based upon their late, beloved leader. They and Mindbender unleashed this new Serpentor on the world, his army headquartered on Cobra Island. They battled Cobra and the reinstated G.I. Joe team until Serpentor was beaten and nearly killed by Cobra Commander. Most believed his body was lost, but the Jugglers managed to recover Serpentor's body, hoping to alter it and have another soldier to control. At the same time, the Jugglers activated their original altered clone in the guise of General Philip Rey and sent him to fight Cobra agents around the world. Even Rey himself was kept in the dark about his true identity, and mental blocks put in place kept him from learning the truth. After he proved himself in battle, Rey was finally placed in command of G.I. Joe, giving the Jugglers a commander they could control. Under Rey's command, the Joes stopped a plot by Cobra to unleash the weapon known as the Tempest, while facing a new threat in the organization known as the Red Shadows. The mysterious group assassinated the corrupt Jugglers and destroyed the body of Serpentor that was in their possession. Once General Rey led the Joes to victory over the Red Shadows, the team was disbanded.

    Cobra Commander's fate was unknown following his confrontation with the Red Shadows. Though the G.I. Joe team did not learn this for nearly a year, Cobra Commander slowly began to rebuild Cobra as he had once before. By means still unknown, he killed White House Chief of Staff Garrett Freedlowe and took the official's place. Now posing as one of the President's closest advisors, the Commander gained unprecedented access to government secrets. He attempted to convince the President that the newly reactivated Joe team was not only unnecessary, but not to be trusted. The President trusted "Freedlowe's" advice and allowed him to create a special missions team called the Phoenix Guard to replace the Joe team. The team's leader was General Philip Rey, who had no idea of Freedlowe's true identity. And unbeknownst to Rey, the soldiers assigned to the team were all former Cobra agents under assumed identities. Rey was told the Joe team had gone rogue, and the Phoenix Guard was soon sent to invade and take control of Joes' new headquarters. Though Rey ordered there be minimal loss of life, the disguised Cobras caused extensive damage to the base, injured a number of Joes and killed even more of their support staff. As his team secured the base, Rey discovered who they really were and helped the Joes defeat the invaders.

    The Phoenix Guard incident left Rey cofused and upset, wondering how he went through with the operation without questioning his orders. He realized that he felt compelled to follow his orders despite any misgivings he may have had. In therapy sessions with psychiatrist, Scott Stevens, he discussed the incident, and violent nightmares he had been having. He was also unable to recall much of his past. While the Joe team was on leave, Rey approached Duke and asked him for his helping piecing together his past. In classified documents, they found the name James Nurss and learned that Zartan's brother Zandar had used the name as an alias. They headed to the Dreadnoks' hideout in the Everglades and after a brief, brutal fight against the Dreadnoks, Rey learned that Zandar had brokered a deal with the Jugglers as Nurss. Zandar then directed him back to Dr. Stevens. Rey and Duke confronted the psychiatrist, but Stevens began using post-hypnotic code words to control the General and ordered him to kill Duke. Before he shot the Joe, Rey demanded the truth about his past. After finally explaining all the details about Rey's past, Stevens revealed that he was Crystal Ball, and had been serving as Rey's psychiatrist for some time. He then told Rey that he could claim the role of Serpentor and destroy Cobra Commander. After being told again to kill Duke, Rey broke free of the mind control and knocked out Crystal Ball, rejecting the identity of Serpentor and asserting, "My name is Philip Rey." As Crystal Ball was arrested, Duke decided that due to the good Rey had done in the past, he would not reveal the truth to anyone aside from General Colton. He added that if he even saw a hint of Serpentor in Rey, he would take him out personally. The General vowed not to let Duke down. Some time later, Rey returned to duty in Jordan, where he led troops fighting Cobra Sand Scorpions during the conflict known as World War III. Rey personally led the team that found the U.S. president in Jordan after he had been kidnapped and abandoned in the desert by Cobra Commander. The president's rescue came shortly before Cobra was defeated and the war came to an end.