Specter kidnaps the Professor, Aki, Sayaka, Satoru, Hikaru and shrinks his laboratory, with Kakeru and Natsumi and who he kidnapped inside. Despite that, the lab is at least small enough to be disguised as a Pipo Helmet, which then Natsumi and Kakeru have to control the monkeys (named Piposaru in Japan) to help rescue their friends as well as defeat Specter.
Unlike other stand-alone titles in the series such as Pipo Saru 2001 and Ape Escape: Pumped & Primed, the game borrows heavily from Ape Escape 3. The same graphic engine is used, which is a first for Ape Escape, as usually all game's graphic's are re-created for each game. In a different approach to the normal Ape Escape gameplay, SaruSaru Big Mission has you controlling the Pipo Helmet shaped lab. By latching it onto a monkey, they can gain control of it, including any abilities it may have. If the monkey takes too much damage, they will lose control of it. The aim is to utilize the monkeys' abilities to reach the end of the level safely.
- The game features monkeys based on Kei and Yumi, which is a possible direct follow up to Ape Escape 3 having monkeys based on Spike and Jimmy, which are based on Spork and Shimmy.
|Characters||Casi · Jake · Natalie · Professor · Specter · Spike|
|Gadgets||Dash Hoop · Magic Punch · Monkey Radar · R.C. Car · Sky Flyer · Slingback Shooter · Stun Club · Time Net · Water Net|
| || |
|Prehistoric Era/ The Lost Land||Fossil Field · Primordial Ooze · Molten Lava|
|Cenozoic Era/ Mysterious Age||Thick Jungle · Dark Ruins · Cryptic Relics|
|Dimension/Dimension X||Stadium Attack|
|Primitive Age/Oceana||Crabby beach · Coral Cave · Dexter's Island|
|Ice age/New Freezeland||Snowy Mammoth · Frosty Retreat · Hot Springs|
|Dimension/Dimension X||Gladiator Attack|
|Recent Past/Medieval Mayhem||Sushi Temple · Wabi Sabi Wall · Crumbling Castle|
|Present-Day/Futurama||City Park · Specter's Factory · TV Tower|
|Present-Day 2/Specter Land||Monkey Madness|
|Dimension/Dimension X||Peak Point Matrix|