Penn and Boone's friendship is put to the test when they both fall for a beautiful alien princess that they must escort though the jungle back to her tribe.

Phyllis has Penn and his team watch a play-back of their just-completed mission in which they were explorers in a race against time to return an idol to a temple while being chased by Rippen and a giant man-eating toilet.

Concerned about his abilities as a leader, Penn and his team are zapped into a world where they are sports balls to teach the other balls to defend themselves from their enemies.

After Boone fools around on the zapping platform, he and Penn swap roles, so Boone becomes the hero.

Penn must overcome his jealousy of popular fellow cadet Blaze to complete his mission and finish at the top of his class at Dragon Flight School.

The kids get zapped into a backyard world where they become military action figures.

Phil and Rippen tunnel into The Odyssey and damage the Multi Universe Transprojector, causing unbalance in the multiverse. Vortexes form in every world that Penn and his team have visited. Penn, Boone, and Sashi must travel to each world and close all of the vortexes before everything and everyone from all the worlds get sucked into nothingness. During their mission, Penn finds a crystal shard in the nothingness, which, according to Phyllis, is the key to finding his parents.

After a recap of the events of the first season. Penn, Sashi, and Boone are sent to a pirate world where whales act as the ships. Penn must get to a treasure before Rippen does, but finds himself teaming with a competitive female pirate in the process.

The trio find themselves in a fairy world in the midst of a wrestling tournament which Penn and Sashi must win to keep the forest out of evil hands. However, things are complicated by an argument between the two, forcing Boone to try to get them to mend their friendship.

Sashi is called in for sensitivity training which Principal Larry forces Penn and Boone to attend as well. The methods seem to work to quell her anger, but soon become a hindrance when the trio return to the underwater world for a mission.

A mission in Cereal Mascot World gets weird when the Milkman makes an appearance.

Penn, Boone and Sashi must stop Rippen from ruining Middleburg High when he switches bodies with Larry.