After...
...visit the Inspector's cabin (downstairs) and he'll ask you to go get the bullet from the Doctor. Go to the medical bay (downstairs as well) and get the bullet there.
You'll proceed through the story for awhile and reach a point where you can finally return to the cargo bay. Examine the right locker and get the screwdriver from the bag in the locker. Use the screwdriver on the crate to get the second bullet.
Finally, return Matt's slingshot and proceed back to the Inspector's cabin. Pick the lock and enter the cabin. Go to the desk and take the bullet. Examine the microscope and use both the bullets on it. Finally, look in the microscope and match the edges.
If you're having trouble picking the lock...