Possible:

Find Magnetic Bomb

Give Bomb To
Clutter

Sabotage Gunboat

Join Dowey for
Getaway

Impossible:

Same
                            Mission 2: Subpen

                   Go into the pump house and get the magnetic bomb.
                   Find Clutter with your scanner & give it to him. Find
                   the gunboat with your scanner and place the other
                   bomb on it. Find Dowey on your scanner and
                   escape.