When hero Adam Warlock takes possession of the artifact known as the Infinity Gauntlet, he expels the good and evil aspects of his being to become a totally logical being, who can therefore use the Gauntlet wisely. This act recreates his “evil” persona and old foe the Magus, who desires universal conquest and revenge against Warlock and the Titan Thanos. (Meanwhile, the effectively emotionless Adam is brought before a “jury” of the cosmic powers and voluntarily surrenders his godhood once he is found to be “guilty” of being unworthy.) The Magus collects five cosmic containment units (another name for the Cosmic Cubes), and with the power gained incapacitates the cosmic entity Eternity; creates an interdimensional realm and an army of doppelgängers – evil “mirror” images of Earth’s superheroes.
After investigating the energy of the containment units, Thanos discovers the Magus and retreats to warn Warlock. Galactus and several of Earth’s heroes also investigate and then attempt to revive Eternity, as the entity will be required to petition the Living Tribunal, who has decreed that the Infinity Gems can no longer be used in unison in the Earth-616 universe. The rationale is that if the Gauntlet can be reactivated, then the Magus can be removed from existence. The Magus sends the doppelgängers to Earth to distract the heroes, and the evil version of Mister Fantastic detonates a gamma bomb when the heroes assemble at Four Freedoms Plaza, however, the Invisible Woman contains the blast while Thunder God Thor directs the radiation into space, and a surprise attack by the Magus and the doppelgänger of Thanos has the heroes believing the two characters are now allied.
The story climaxes at the Magus’ base: a group of heroes free those who were replaced by doppelgängers; cosmic adventurer Quasar arrives with the Ultimate Nullifier (with Thanos goading Quasar to use it against the Magus knowing that Quasar would also be destroyed) and villains Kang the Conqueror and Doctor Doom appear, hoping to harness the source of the powerful energies detected.
Warlock and the still inactive Gauntlet are captured by the Magus, and both attacked by Doom and Kang. Warlock is defeated and the Magus is severely weakened in the battle and attempts to use the containment units but discovers they have been stolen. Doom betrays and stops Kang, and then demands the Gauntlet from the Magus. Eternity, however, has just been revived and has requested the Gauntlet be reactivated, which the Living Tribunal agrees to. An apparently omnipotent Magus easily defeats Doom and dissolves Quasar, who arrives with the Ultimate Nullifier. Thanos defeats his doppelgänger and distracts the Magus, allowing Warlock to grapple with the villain for the Gauntlet. Warlock releases from the Gauntlet a being that is a composite of the entity Eternity and his twin, Infinity. The being incapacitates the Magus, allowing Warlock to absorb the character into the Soul Gem. The experience places Warlock in a coma.
Thanos reveals to the assembled heroes that the Magus was tricked and never gained omnipotence as the Reality Gem on the Gauntlet—which Thanos is revealed to be the secret guardian of—was a convincing fake. The heroes return to Earth and the final page of the last issue reveals that the containment units have been stolen by Warlock’s “good” persona, the Goddess. In addition to these developments, Eternity—who is apparently ‘deputized’ by the Living Tribunal to make such a decree—thereafter declares that the Gems on the Gauntlet will never be able to be used again as a single unit, no matter what future crisis befalls the universe.