Taxi down U.S. 101, turn right at highway 92, pull up to the EA headquarters and blow it away!
Select option 2 {FREE FLIGHT, NO ENEMY CONFRONTATION} from the main menu. Then select zero instead of 1 to 4. The screen will go into a spiral and scroll way south to 34 by 117 degrees, placing your plane somewhere without a runway. This happens to be in the middle of edwards air force base, where the F/A-18 was flight tested. To take off you have to use the afterburners. 117 degrees is the furthest south you'll be able to fly, but you can go in other directions. Is there more to this back door?
In mission 6, once you've fired all your missiles, you can land on the shadow sub (if it's still afloat) and it will refuel and rearm you.