Jumping Flash! 2: Big Trouble in Little Moo follows the adventures of Robbit, a piloted flying robot rabbit. The goal is to save all the moo-moos, little alien creatures, and get to the exit.

Baron Aloha, the villain from the original Jumping Flash! game has returned to his home planet of Little Moo to plan his revenge. When all of a sudden a gigantic space alien named Captain Kabuki appears and starts to take apart Little Moo piece-by-piece and start a small collection of "snow globe" type ornaments made from the fragments of Little Moo.

Baron Aloha escapes from Captain Kabuki and calls upon the help his arch rival, Robbit, at Universal City Hall. This is where the player comes in.

The mission is to jump from world-to-world, putting the pieces of Little Moo back together, rescue the Moo-Moos, and ultimately defeat Captain Kabuki.