Jake goes out to a forest behind his home to go camping. While camping, he watches shooting stars go flying past, but one crashes into Earth not too far away from him. Jake finds the Rognitrix and it climbs up a stick and attaches itself to Jake's wrist. Jake must now figure out it's powers
Jake and Robert go to a carnival and meet a homeless Norpholian. Jake convinces Robert to let the Norpholian named Kogan stay at their house, then he steals everything in the house and Jake & Robert must go after him.
A distant relative of Jake's comes to stay at their house, little do they know that this relative is being possessed by a speed-freak alien. While Jake's parents leave, it reveals this to him and says it will leave his cousin alone if Jake can win in a race. The Rognitrix continuously mistransforms Jake and he must race in those forms until he finally is able to become VLOCT to win. The alien then leaves Jake's cousin and his cousin promises to keep Jake's secret a secret.
Jake finds out that while Will was being possessed he called on bounty hunters to find Jake incase his plan didn't work. Jake and Robbie now have to battle their way through five different hunters who also happen to be in Jake's Rognitrix!
A week later, after hearing that his bounty hunters failed, the ghost that possessed Will returns and possesses Marty, refusing to race or leave until Jake hand's over the Rognitrix. Jake becomes his thirteenth alien and must figure out it's powers as he fights Marty.
Rage is being mind controlled by Drogan and returns to attack Jake. He forms himself into a tidal wave and floods Jake's house. Jake must save his family and Rage and then put an end to Drogan. Jake's parents also find out that Jake wields the Rognitrix.
While Jake and Robbie are having a usual day at school, a bunch of books come to life and begin attacking the students. When the school is evacuated, Jake and Robbie step in to deal with the pestering books.
A giant mutant mole is unleashed in Jake's city. He and Robbie fight it and discover it is robotic. After they encounter another one, they try to track where it came from. They find three men dressed in mole costumes, trading alien tech and using the moles as cover ups.
While traveling through the universes, a group of Trapano get very hungry and land on Earth. They begin eating through to the Earth's core, causing earthquakes throughout Jake's town. When Jake investigates, he discovers the group and finds out that they are going to eat the entire planet. After Jake get's knocked out, it is up to Rage and Robbie to save him.
When Nate takes a day off, he decides to take Robbie and Jake to a water park. After they arrive, they find out every single ride is broken. Jake becomes Hyper Pack to fix them all but loses his pack, and then gets kidnapped. Worst of all, the Rognitrix won't time out!
Season 2 Premiere: Rage returns to the surface and pleas for Jake and Robbie to deal with yet another dictator. When Jake and Robbie go underwater, they find that they need to deal with one of Jake's first villains, Kogan.
Kogan has returned and this time he is on Deep Crusher's home planet, Grimentia. Jake and Robbie take their first spaceship ride to remove Kogan but find out he has planted mind-controlling helmets on most of the animals.
Nate takes Jake to work with him, hoping his son will some day follow in his footsteps, but Jake's Rognitrix temporarily shuts down while the office is attacked by uPads (explained later) with just Jake and Natahn around. Jake must then be like Robbie and fight with swords until he can finally access Overflow to take over the master uPad.
All Locked Up is an episode during the middle of season 2. An evil genius kidnaps Jake and hacks the Rognitrix, locking out 15 of his alien transformations. He then locks Jake in a small room with a tiny tunnel at the end that a cat passes through. Jake scans Unnamed Alien and escapes, leading to the arrest of the scientist.
Jake and Robbie are kidnapped by a deranged man. The man hacks into the local news station and begins streaming videos of himself harming the boys on live television. When he discovers Jake's Rognitrix, he chloroforms Jake and begins experimenting with it. After a while he attempts to take it off Jake.
After it all sinks in just how serious the situation, Jake explains it to Robbie. Robbie doesn't take it too seriously until Marty goes missing. They begin the big battle where Jake scans Woof and Squawk.
Jake and Robbie fight with each other while watching Dragon Ball Z. Jake becomes Overflow and hides inside the TV. Then he falls into it. All of his aliens escape the Rognitrix and he instead becomes a Siayan. He must find all his aliens and absorb them back into his tail before anyone else from the Dragon Ball Z universe does.
After Robbie continues to run off Jake starts thinking that he is talking with the enemy. Jake follows Robbie to an empty field. Wishing he had a rabbit transformation to blend in and spy, Jake transforms into Slug.