Several portals leading into the Phantom Zone can be found in the Fortress of Solitude stage. Combatants can be knocked into a Phantom Zone projector and then spat out of a portal, taking damage. They can also be knocked into the Zone itself through a portal at the far left side of the menagerie section, where they will collide with one of the crystal fragments housing a monstrous wraith. The wraith will proceed to take a bite out of the fighter's shoulder before being knocked off by a floating rock, and then the fighter will fall through a second Zone portal, winding up in the laboratory section of the stage.
Zod is able to temporarily trap his opponents in a Phantom Zone crystal as part of his of gameplay and even summon the wraith from the stage transition as his Character Trait.
According to some character profiles, the Phantom Zone is used by Superman to 're-educate' several super-villains into joining his side, suggesting that the Man of Steel spares villains if he believes they could be useful, such as Bane and Killer Frost. Near the end of Story Mode, the Zone is used to safely seal away the Regime Doomsday after the monster is defeated.
If Classic Battle is cleared, a cutscene will show Superman being sucked into the Zone's portal in the menagerie. As he is pulled closer to the portal, he has several flashbacks of Lois Lane, her death at his own hands and his murder of the Joker before being pulled into the Zone by a Phantom. Kal-El is then seen trapped inside a crystal, screaming in anguish as he is banished deeper into the Zone.
- General Zod
- Bane (Regime) Released
- Killer Frost (Regime) Released
- Doomsday (Regime)
- Superman (Regime), Classic Battle or Absolute Justice Only
- Originally in the Pre-Crisis era of DC, the Phantom Zone turned its inhabitants into literal phantoms, who were unable to interact with the outside world but could still observe it. The modern Post-Crisis Phantom Zone was influenced by the Richard Donner Superman movies, which depicted it as a glass shard where inmates were trapped in and flung into space, unable to escape.