You're in kind of difficult situation - tied in chains and with head down, on the Organons' cruiser. Click twice on the Chain and Rufus will get up. Then enter the Chute. You'll find yourself on the outer part of the ship.
Notice that also your Suitcase has survived the trip. Open it and take out Provisions and Socks. Take a look at three Hatches at the bottom of containers. The right one is dirty and Rufus doesn't want to play with it. In the middle one you can see some Cogwheels and the left one can lead inside the ship. But Rufus can hurt himself, trying to open it with bare hands.
Open the inventory and use Provisions on the middle hatch. A hatch over it will open and a Maintenance Arm will appear. It starts to clear the wheels out off wasabi nuts. Take a look at the open, metal part and put Pair o' Socks in it. The hatch starts to close but it won't be able to do it because of socks. Now open the Hatch with Sock and take the Maintenance Arm. Use the Robot Arm to cut the left Hatch. After that you'll see a nice girl named Goal and group of soldiers, who threaten her. Rufus would like to be a hero ... So get In the Hatch and you'll find yourself in the control room on the left. Use the left or the middle Lever and watch the cut-scene.