Had a nice rest? You have just been taken out of your criostasis chamber. Alot has changed. The thugs have managed to get the ninjas to betray us. Did you have problems with your pilot? The ninjas are well known to turn on you. They have turned you in for a large sum of money to the thugs. So get out, get to the bottom of things, get to the crystals that will start the plane.
Good luck!
If you haven't played the first one, just paste this link in your bar: http://sploder.com/?s=thjaa9bb