Eternal Missions enable the player to replay a story mission which was previously completed without a time limit or any restrictions. They are accessed by capturing all three Pink Elebits in a given mission.

As Eternal Missions have no end condition, they will continue until the player manually "gives up" from the Pause menu. The Eternal Mission complete screen displays the time taken to "clear" the mission, the percentage of Elebit nests found, the percentage of power restored, and the total number of captured Elebits.