Seeking to co-opt the near-limitless power of the Source, the evil space tyrant Darkseid continues his efforts to break through the Source Wall. Thinking that the energy associated with the Phoenix Force can help him penetrate the mysteries of the Source, Darkseid sets into motion a plan to recreate the Dark Phoenix by tapping into the memories of her former teammates, the X-Men, as well as drawing the residue of her power from a variety of sources, and then amplifying that residue, using energy streaming from the rupture of the Source Wall. With his help, Metron had pierced the Wall and his sacrifice effected a small rupture which bled a steady stream of energy. Both superhero teams are alerted to the dangers by the Titans' Starfire, who has knowledge of Dark Phoenix's immense destructive power.

Despite their best efforts, each team is defeated and captured by Deathstroke the Terminator and Darkseid's shock troops. Darkseid brings the Dark Phoenix back to life. Both super teams work together, freeing themselves and defeating their enemies in a climatic battle. Colossus prevented the gathering of psionic residue at a Western mesa and this resulted in the Dark Phoenix simulation being flawed, and exploiting said flaw enables the two teams to drive a wedge between Dark Phoenix and Darkseid. Professor X and Cyclops convince what is left of Jean Grey's human consciousness that she is being manipulated, and she once again sacrifices herself to defeat Darkseid, repairing all the damage in doing so.

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