Changes

{{Quotation|Well, so far, so good, Captain EO. But, I must admit that I am a bit surprised after the mess you made of your last mission. But now that you've found the beacon, take the map, find the Supreme Leader and give her the gift. You do have the map, don't you?|}}

Although Hooter had earlier eaten the map, the crew sets out to find the Supreme Leader. As they walk through a hill of garbage (and Hooter insists on putting a trash can on his head to "disguise" himself), the team is ambushed by guards and taken to the Supreme Leader. After arriving, The Supreme Leader (a metallic woman hanging from the ceiling by cables) orders the crew to be turned into trash cans, while Captain EO is to be tortured for 100 years in her deepest dungeon. An unfazed Captain EO announces that they accept their punishment, but tells Supreme Leader that she is beautiful and it is his gift to her to unlock that beauty. EO then points to his ear, cuing the crew to get ready. At this point, music begins and Minor Domo transforms to a keyboard synthesizer. During the transformation, the robot kicks off his leg which transforms into a guitar played by Fuzzball (a flying furry creature), and the rest of his body becomes a drum set played by Idey and Ody. Just when everything seems to be going according to plan however, Hooter slips and crashes into the synthesizer. The Supreme Leader then sends her troops in, but Hooter fixes the synthesizer just in time and begins to play. With this, Captain EO is energized, and he pushes away the guards with a pulse of energy.

At this point, "We Are Here to Change the World," (a song written by Michael Jackson for this film) begins. During the introduction Captain EO transforms various minions of the Supreme Leader into dancers that join him in the song. Eventually the Supreme Leader sends in her "Whip Warriors" (two soldiers who attack Captain EO with electronic whips) while "We Are Here to Change the World" quietly continues in the background. Although he struggles for a while, Fuzzball ties the two whips together, incapacitating the warriors and allowing Captain EO to use his energy powers on them. Captain EO then transforms the prisoners trapped in the walls into another group of dancers, as the song continues in full force. Captain EO next flies up to the Supreme Leader and transforms her into a beautiful woman, before using his energy to transform the lair into a beautiful palace with Greek columns. With the sun now shining, everyone celebrates as “Another Part of Me” (the second original song in the film) is performed. The film then ends with the triumphant crew flying off towards their next mission.