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 return to the dragon world which finds itself under attack by winged unicorns which threaten to destroy Wingfire Academy. However before the team can fight them, they must get Blaze, who has fallen into a slump from a previous defeat by the unicorns, back on his feet to help them.
The trio is transported onto a space ship whose human occupants are set to arrive on a new planet to colonize. However, Penn finds himself in the form of a mouse and must save the ship from a feline Rippen who seeks to plunge it into a black hole.
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.
Boone and Sashi have to build a Penn robot to save a world from the forces of evil.
Team Zero return to the Ball World to save its past from Rippen.
A return to the Knight World causes issues for Boone when he meets a better wizard than himself.
In a world that is a Rock, Paper and Scissor version of Game of Thrones, Penn's team face a siege by the Scissorian army.
Penn's team has to save a ghost from supernatural exterminators Rippen and Larry.
Penn has to take care of The Chinchilla -- which causes problem on their return to Plush Toy World.
When Sashi's parents find out about her real job with Penn and Boone, Penn has Phyllis zap her and her parents into the Outer Space World.
A mission in Cereal Mascot World gets weird when the Milkman makes an appearance.
Penn's emotions cause problems for the latest mission.
Penn, Boone, and Sashi visit an anime dimension to compete against Rippen in a ninjutsu tournament to bring back an island back with the help of 3 new friends.
Penn has to stop Rippen from ruining a dinner in a sitcom dimension.
Penn, Sashi, and Boone must make the Princess Argelbleccht and Grinkon fall in love.
Boone is kidnapped and Penn and Sashi must solve the mystery and find him.
Vonnie must rescue Brock from the belly of a giant chicken.
Penn, Boone and Sashi must stop Rippen from ruining Middleburg High when he switches bodies with Larry.
Boone gets a bad report card from Phyllis, making his parents mad. He tries to fix this while on a mission in the Giant Monster World.
Rippen's origin story is revealed for his first day as a part-time villain.
Penn, Sashi, and Boone must travel to the three most dangerous places in the multiverse in order to free Penn's parents as Rippen plans to conquer the Most Dangerous World Imaginable with Larry and those with him after having to close its portal from the other side.