This is THE MOST HATEFUL puzzle in the entire episode. You essentially want to grab the bazooka up top, snag a missile from the open crate in the middle, combine the two in your inventory, run up to where you got the bazooka and blow the robot away. Once you've taken the robot out, you can cross the water, grab the blowtorch, take it back to the sub and burn your way in.
But with the bot shooting at ANYTHING that moves, it's not so easy. You need to create a distraction when you run up to where the bazooka is. Something that will give the robot LOTS of tiny little moving targets while you run and get the missile and combine the stuff. And you'll need to do it twice.
Cause some BUGS in the system. Hint. Hint.