The first time I beat this level, I just destroyed all of the enemy ships before the timer hit zero, and the freighter started working again. After reading the "Acts" section related to this mission, I redid the mission, docking my wingmen to the freighter. According to the acts (under the mission "Antimatter Cordon") the countdown will pause if one ship is docked, and the confinement will increase with two or more ships docked. Use this to keep the freighter from exploding, and keep the enemies from getting to close. (Deathblow remote missiles are very helpful.) After a number of waves, the enemies should stop coming, and you can proceed with the mission.
The acts says that "Once you have reached the L - Point. You will/may find the exit blocked by aliens, You need to release the antimatter container casing and send it in direction of the L - Point. When it's close to the L - point, detonate it to eliminate all aliens close by. You can then continue through the Formalhaut L- Point." I have not encountered this before, and I would like to, since it is part of the game.
This is one tough navy, boy. They don't give you time off, even for being dead. -Clay
Storm Petrel
Campaign 1: The Minbari 
