Return to the Hulk
Shadow Team's objective is to sneak into subspace past a Vasudan patrol, and avoid detection from the GTVA Research Teams within the subspace corridor towards Altair and get scans from the Lucifer-class SD Nyarlathotep for the "employers."
Bring whatever ships you want for Shadow Team (a four-ship formation), the above line is a lie, just be sure you have something for intense combat. However, your #2 (your Shadow CO) and #3 (Lt. Mackie) will be invincible.
The Qualmotep will call Shadow Team and tell them to break off (as the Altair jump node has been sealed off from all traffic), and you will have Vasudan fighters bearing down on your team. Just evade for a minute or two, and the Escher will arrive on the scene, and this whole mess will get sorted out.
Then a Charybdis and two Science Vessels will come out panicked from the scene. One of the science vessels die by self-destruction. Your job is to help defend the convoy. And you'll have to engage Erinyes-class fighters and Athena bombers. As much as you have to wonder where they came from, your priority is to kill all you see until the vessels you need to guard safely get out. Don't worry about the Escher, it will provide fire support for the convoy.
Thought this was enough? By the time the Escher is ready to get into the jump node, four Bonarges bombers come out of the node, along with escorts. Focus on the bombers. Then more Bonarges come out, do whatever you need until the Escher jumps into the node (by that time, they will bail out too). Once all threats are dealt with, you will have the order to return to base.