The final level is split into three parts.
The first part is the most difficult to execute. Use the antigravity suit to get to the edge forming the upper level. Watch out for the launcher on the ceiling, if you get hit by its shots your vest will spuriously turn on.
There are three colored bins along with color ball launchers. Blocking each bin is a large robot. To get rid of the robots use the rocket turret placed along the edge. Once the robots are gone, it's a simple matter of using the attractor spheres to get the balls into the bins. Or at least it would be, was the aim of the red ball launcher not busted. You will just have to fiddle with the timing of when you enable the attractor sphere until the ball manages to hit the bin.
With the bins hit Craven will appear and run away, follow him into the now open door.
The second part takes place under water. There are three huge colored balls and matching bins. Due to their size they barely move even when shot with the helper hand, so just keep shooting them until they are in the bins. With all three bins set the floor will start to raise. Don't get squashed against the ceiling and you will enter the final part of the level.
The third and final part is anticlimactically just kicking two colored balls into bins to open the door. Once the door opens just follow the lit path to the submarine and jump onto it to finish the game.