This is what I got so far...
Mission 1 - NTR (Neo Terran Remnant) have been raiding cargo depots in the Polaris system. Intel has pinpointed several likely future targets, and has rotating shifts watching them. Your squadron (luckily enough) happens to be there when the NTF make their move.
Alpha wing arrives to releave another wing of guard duty (Gamma, Kappa, etc...).
Alpha is atracted deeper into the cargo depot (so it has to fly around, in case the pilot just wants to sit around waiting for the enemy to appear) by some routine cargo or freighter scan (I'm still thinking how this can be done without making it boring).
There are a number of freighters working around and when the player has succeded in being lured into the cargo depot a freighter will arrive (Triton so it can resist a few punchs or maybe a Poseidon if I can make it survive a few seconds) and soon after a wing of Lokis will arrive with the objective of blowing the before mentioned freighter up. Alpha is lured to an oposite side of the field and when the menace is almost defeated in the other side of the field appears 2 wings of Lokis and 2 Poseidon freighters trying to steal two specific cargo containers. Alpha must finish off the first menace completly (if he hasn't done it already) and try to stop the freighters from stealing any cargo. I'll try to think of something to make sure Alpha's job doesn't become just blow the freighters up as quick as possible so he doesn't just focus on the freighters but also in the two wings of Lokis flying around (possibly stopping the lokis from destroying something else also).
As soon as this is done the mission should end unless one pulls something like in the FS1 scan cargo container mission where an enemy Elysium (unknown until the debriefring) steals another cargo container. It may look a bit careless by Allied Command so I'm not sure about this part.
I'm having a bit dificulties making a diverse, yet suficiently large, yet believable cargo depot. The best I've done so far is this:
EDIT: changed to lvlshot as requested
Yet is doesn't look very diverse in terms of diferent cargo containers
I'll try to improve what I got so far...