This issue opens with the Watcher telling the story of the ill-fate of one of the “most advanced races in existence”, the “Taa”. Billions were dying of an incurable plague. The few survivors flee in search “for the face of the infinite”, to “preserve” “some vestige of [their] glory”.
Back on Earth, Lilandra, Empress of the Shi’ar, calls upon Xavier and the X-Men for help. The M’Kraan Crystal and the “nexus of realities” has been disturbed, and she needs the help of the Phoenix once more to “halt M’Kraan’s destruction”. Xavier is fearful of allowing Jean to summon for the Phoenix once more as they were barely able to expel Dark Phoenix from Jean’s body the last time the Phoenix was summoned. Despite the risks and objections, Jean agrees to help Lilandra once again as Phoenix.
Lilandra has the X-Men teleported to her Shi’ar palace. There, Jean summons the Phoenix Entity to assume her body once more. The Phoenix plans to heal the M’Kraan Crystal from the inside, and that is where the X-Men, with Gladiator, proceed.
Elsewhere, the Dweller puts his plans in motion. The N’Garai and a resurrected D’Ken attack the X-Men from inside the Crystal. The Phoenix is stalled from healing the Crystal by the attack.
Fuelled by the combined “essences” of the X-Men and Gladiator, the Phoenix summons enough strength and “sends froth wave upon wave of all-encompassing, life-affirming telepathic energy”. It is the power of hope that finally vanquishes the “Black Stain”. For a moment, balance is restored to the nexus, then the Crystal explodes and extinguishes all life.
As the last of the Taa tries to “outrace the final wave of destruction”, he becomes one with the cosmos to become Galactus. Dweller is expelled once more into the depths of darkness.
The universe is once again reborn, overseen by the omnipotent Tribunal, and the brothers Alpha and Omega. Evolution on Earth cycles through once more, and the story ends with the beginning of the founding of Xavier’s Institute once again.