Near death, the sole survivor of the destruction of an orbiting space station is rescued by a group of aliens who observe the earth from a secret sub-Arctic base. The aliens have been monitoring human evolution, which they claim to have initiated millions of years ago through the deliberate mutation of prehistoric apes.

Incorporating some of the aliens' technology into his flight suit, the astronaut escapes from his captors. On the run, he stops to use his stolen powers to aid a disaster-stricken Reykjavik, Iceland... thus alerting the aliens to his location. A battle ensues, and the aliens' installation is destroyed in an atomic explosion. Reykjavik is leveled by the shockwave.

On a rampage of revenge, the alien survivors set about the task of destroying all human life on earth, which they have now deemed a failed experiment. Beginning (of course) with New York City.

In issue #4 (with new writer Gary Friedrich at the helm) the title changes to Phoenix...The Protector. Blaming himself for the alien attacks on Reykjavik and New York, and despairing of any hope for the future of mankind now that the aliens are on the warpath, Phoenix carves a tombstone for planet Earth and launches himself into space at full power, planning to burn himself up in the atmosphere.

Rescued by yet another group of aliens (The Protectors) Phoenix is given a choice. Revealing themselves to be the masters of the previous group of aliens, the Protectors offer Phoenix the opportunity to prevent the termination of all human life on Earth by proving they are "worthy" of life. Given a new costume, new identity and new powers, Phoenix has become The Protector.