Spongebob, along with his friends who have joined him, travel to the Central Park Zoo and meet Alex and his animal friends and get lost on Madagascar, meeting new allies like partying lemurs, commando penguins, aliens who sometimes get on eachothers nerves, and to see whats beyond the zoo, while they must fight returning enemies, the Foosa, and a mutated demonic cobra named Lord Cobra (not the G.I. Joe one, an entirely new one)
- I Like To Move It- By King Julien and Lemurs
- If I Didn't Have You- by Monty and Seven11
- In The Dark Of The Night- by Lord Cobra and Villain Leaguers
- Animal I Have Become
- King Simba, Timon, Pumbaa, Queen Nala, Prince Kovu, Princess Kiara, the lions and hyenas (reformed) from the Lion King make a suprise appearance toward the end of the movie. Monty reveals that he took the time to beam their animal friends from the Pridelands to Madagascar to help them battle the Villain League.
- The song "If I Didn't Have You" from Quest For Camelot is sung by the Hyenas and the aliens Monty and Seven11 (dubbed as Devon and Cornwall from Quest For Camelot)
- The song "In the dark of the night" was sung by Lord Cobra, Zira, Plankton and the Foosa as back up singers, as Lord Cobra planed to awake the Monster within Alex the lion, causing him to turn on all his friends.
- Alex, Marty, Gloria, and Melman join Spongebob and Friends as members of their Shell Louge Squad in later adventures.
- Lord Cobra will appear again in SpongeBob and Friends Go on the Quest for Camelot, resurrected by Dr. Facilier, who fuses Excalibur with his arm, and will be defeated again when Shenzi backflips over the stone and Cobra will impale it into the stone and be vaporized forever.
- Nala only has the role of yelling, "Charge!"
- Shenzi did not know destroying the meddailian would result in Destroying Lord Cobra, She wanted to break it to see Lord Cobra slither away like a little girl.
- Monty and Seven11 are based on Devon and Cornwall, but with defferents, like they're not conjointed dragons, but bickering aliens.
- there was an alternate verson of part 2, at the end, Alex said: "Spongebob has another song for you." and Spongebob began singing New York, New york, with a voice simuler with Frank sinatra, but that verson was removed by WMG, and it was replaced with what really happed after Marty said his peace.
- after Alex realizes he became a monster and ran off, what a beauteful world was replaced with the animal i have become because Supervideomaniac back then thought it would be cooler and much more fitting.