Go to the select mission window and select the mission 'Test Launch a Probe and Collect Data' Once in the simulator select, from the control bar to the right of the screen, Accelerate. Go to any of the difficulty levels,and then go to the 'Fleet' screen, and select a fully loaded ship(must have 2 torpedo launchers and all types of probes, best to use a Galaxy, Intrepid or Excelsior class ship). Also, when you pick your class of ship, the hull mainframes will be empty. With an advanced playing level, you are also granted the use of ablative armor and a cloaking device.
For instance, the Defiant class ship's original defense mechanisms only included a navigational deflector and shields. If you play under the difficulty level of 'advanced', you will have a wider selection of parts for each vessel you decide to use. In order to accomplish the 'Destroy The Planet Killer' level of the game/simulator without destroying your ship you must have it equipped with 'Tricobalt Torpedoes.' (Be warned: Not every ship can support the use of 'Tricobalt Torpedoes.' If the ship sent on the mission is not equipped with these, it will be destroyed!)