You start out the game as two very bored characters who have nothing to do now that the galaxy is safe. Luckily, a guy named Fizzwidget who can't talk properly teleports you to the Bogon galaxy. He wants you retrieve a fuzzy blue ball. Well actually it looks like a Tribble from Star Trek. You say sure!
Off you go to your very first planet - Planet Aranos. This is in essence a training planet. You have a few basic weapons - the lancer, gravity bomb, wrench, etc. Go step on the elevator (circle shape) to go up.
In the next room, shoot the guys with the CIRCLE button, and gather up the nuts and bolts. Those are your currency for buying weapons, ammo and other items. Go up the next hallway and kill a few more enemies. There's a health recharge at the end of the hall. Be sure to always shoot or bash all boxes you see to get ammo, and anything breakable around you for bolts.
Head out to the outer area. There are bombs here. Hit the lights for more bolts and go up onto the elevator. "Use the gravity bomb here". Good idea, it's in essence a grenade. Go into the door and find the fuzzy blue creature.
Ms Ninja is upset with you. I have to say it was VERY obvious to me from moment one that this was a chick ninja. Anyway, shoot the enemies that remain when she escapes and the door opens. Slide down, blast the enemies with a gravity bomb and go into the window.
You see a video of the ninja. She wants security to help her out. Now you're in a room with health and lots of enemies. Blast away! Go up the elevator and into the hallway. Now you're in another room with more enemies and a health. Clear it and head on.
Next you're in a room with several doors. Enemies blast through them. Fight them all. There's a scene with you surrounded. You run and jump - and are caught by your spaceship.
You see a video of ninja-chick stealing maps. On to the next planet!
Ratchet and Clank 2 Going Commando Walkthrough