Danny's new ghost powers are put to the test when the school cafeteria's all-vegetarian menu arouses the ire of the ghostly Lunch Lady, a 50-foot shambling pile of mystery meat who seeks revenge and a return to high-cholesterol diets. It's up to Danny to push her back in the fridge where she belongs.

Skulker, a predatory ghost hunting legend who fancies himself a collector of all things rare and unique, has set his sights on Danny Phantom, the world's only half-ghost/half-human hybrid. The games begin, as good and evil ghosts face off.

The building boom in Amity Park upsets Undergrowth, the ghost of all things plant-like and vegetative. The green-thinking ghost takes over the town, turning everyone into plants themselves. All except Sam, that is, whom he makes his Earth-loving queen. Unfortunately, Undergrowth brainwashes Sam and uses her to attack Danny! Danny, meanwhile, has been battling a nasty case of the chills that leaves him too weak to fight. Escaping from Undergrowth in the Ghost Zone, Danny turns to his cold-loving friend, Frostbite,who explains that Danny is developing a new power. Now, Danny must learn to master his new freezing skill so that he can make his way back to Amity Park and pull the town out of Undergrowth’s leafy clutches.

After getting lost in the ghost zone, Danny and his friends find in a frozen zone the Infimap, a map that lets the holder to travel everywhere in the ghost zone. After Vlad Masters steals the map, Danny, Sam and Tucker must chase him through different times and places, from Salem to ancient Rome, to get this treasure before he manages to conquer Earth.

Amity Park is in the midst of a drought, and Mayor Vlad, eager to score points, releases Vortex, the weather ghost, to make it rain. But when Vlad double crosses Vortex, the ghost conjures a storm that threatens to drown the town! As Danny Phantom flies to the rescue, he’s zapped by a lightning bolt. When he comes to, he discovers that his emotions are now directly tied to the weather!

Amorpho, a ghost with morphing abilities, impersonates people and gets them into trouble with it. He then impersonates Danny and both of them must learn the price of fame when a fenton device interrupts some of their powers, preventing Danny from returning to his human self and locking the evil shapeshifter in a shape that calls too much attention: Mr. Lancer's.

Danny, after being publicly shamed by Vlad's new ghost hunting team, wants to be normal again. So he gets rid of his powers by reactivating the Fenton Portal after Jack dismantles it for a software upgrade. However, an asteroid made of Ectoranium threatens the Earth, and Vlad - after revealing to everyone that he is Plasmius - fails to stop it. The world now relies on a powerless Danny to get help from the ghosts in the Ghost Zone!