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The story of Ape Escape: Pumped and Primed is as follows. Spike the protagonist of the Ape Escape franchise and his friends, the good Professor his assistant Natalie and the Professor's computer AI Casi, all showing up at some virtual tournament where they see some old friends, the Pipo monkeys. They also encounter some new competition in the form of the hot headed raining champ Helga and the mysterious black and primary colored Pipotron. After a humorous opening cutscene the player selects their character and begins the first tier of the tournament, after completing these challenges Spike's best pal and one of his worst enemies, Jake turns up under the control of the usual antagonist Specter to aid the Pipo monkeys. After a short boss fight with Jake you move on to the next tier of challenges and after a few "wash rinse repeat" segments where you fight Jake then compete in the tourney. Eventually you fight Specter but make no mistake he is not the villain of this game shortly after this fight someone wins the trophy, regardless of who wins the Pipotron get the trophy and give the data disk inside the trophy to their dark master The Grid Core who then in true villain form betrays his minions and replaces them with Pipotron who are 100 times more powerful than the "originals". The player then competes in an evil version of the tournament playing more evil versions than the original tournament events gradually working their way to Grid Core's lair fighting "dark versions" of Jake and Specter. Once you reach Grid Core and defeat him the virtual world is returned to its previous glory, Jake turns good and Specter turns... less evil and Spike has a crush on Helga.
Game play follows the trend of previous Ape Escape titles, you have a set of tools usually used to capture monkeys now used to whale on them and the other contestants. Each tool makes interesting use of the two control sticks, one tool will have you thrusting the right stick forward to hit something others will have you spinning the control sticks in order to control a rowboat. The tournament theme of the game turns it into a minigame collection of 5 or so game types based on the different tools in each characters disposal. The game also utilizes "the Monkey fan club" a system that rewards you with various gifts based on your performance in each game giving things like letters, character skins, ally characters, weapons and new skins for each tool in your disposal.