There's several triggers here, it's hard to tell you what to do when you just tell us you're in this system (especially since there are two versions of this mission AND several possible decisions you can make, but the OP mentioned "escort convoy" so I'm guessing you're on the NESF side, not MSF). So I'll just tell you everything that happens.

1. Portal into system. Continue escorting the transport until it reaches the station. Sometimes when you reach the station nothing happens, so you have to move your mothership manually a little closer to trigger the next part of the script.

2. Some dialog happens and you have a choice to make. Whichever you choose, the attackers from the portal and the fleeing transports must both be destroyed. Players who failed somewhere along here likely missed the transports or killing all the attackers in time (there are two waves of attackers). Strangely, if you stray away from the station too far during the first attack (iirc) you will also lose. Caution: I'm not 100% sure of this - but I've never "mysteriously lost" this mission when I leave at least 1 fighter in sight of the station. (Actually, I've never lost this mission, period, but usually my team is strong enough to breeze through this - gen 5 ships, nearly maxed pilots, etc).

3. Move to the staging point. Don't be slow. There are allies following from the rear but they don't exactly follow you / wait for you. I never arrive after them so I don't know what happens if you're late (and why take the risk to find out?).

4. Move to the portal and engage the fleet in battle. If you have any long range missiles or torpedoes, fire all of them before you get close. It's a nasty fight. (It's actually not that hard but I've played several times already and usually by this point I've already gone grinding for loot and exp.)

5. Escort the transports from the other station to the portal.

After that just jump through the portal and continue in the next system.