The Doomsday Missile works the same way as a Tactical Nuke from the base game. It can only jump from a friendly City to City in order to nuke enemy solar systems. Obviously building these on "scarce" solar systems is a complete waste of Hammers but given the time to prepare, you can build a Starfortress to increase your influence and to produce anti-ship missiles every 15 turns. This works as a safe for Missiles, Nuclear missiles included.