The RTMod uses a couple things for ending missions.
1. No Warp Effect is selected for Alpha Wing, that means no warp hole.
2. You should set the arrival/departure points for Alpha Wing to the hangarbay of a ship. (And reset it at times 'cause FRED2 has a habit of forgetting what it was set at.)
3. The actual SEXP code first disables the player's jump drive at mission start. (break-warp) After the goals are finished, when the distance between the ship you select is less then a number you set and the player is facing the ship and the player has targeted the hangarbay subsystem, then you can fix Alpha 1's jump drive. (fix-warp) You should also let the player know they can leave.
4. When the player hits Alt+J, you'll hear the drive power up and then the game will cut to debriefing.
With the end-mission SEXP and other stuff, all this could be improved. I also made a more advanced landing system, supporting multiple possible carriers, that I put online. (I'm not even going to try and explain that in here.) It's setup for the RTMod so if you don't have it, you'll get quite a mess in FRED2.
http://members.aol.com/ariskalzar/Watchdog.zip