Some mission ideas :
1)
There is a strike at Freedom shipyards, Polaris. The shipyards have been bought by Akheton SDG and the rumor says they will fire the Terran workers. Vasudophopic speech is all over the civilian information network. The small vasudan tech crew is locked down inside the control center of the main Arcadia installation.
You have to escort an argo with the Polaris military police to the installation, destroying cargos arround the docking point to clear the path. The argo successfully docks, but the MP refuses to open fire at the shipyards workers crowd.
Then, some workers try to get to the Iceni (not complete yet) and sabotage it, you are ordered to disable their shuttle, but it blows up (that was an accident). The situation is still stuck aboard the Arcadia, but the shuttle inccident makes it turn bad : the workers start to depresurize the control center and will stop only if the shipyards are nationalized by the polaris government.
Then Bosch shows up with an Orion destroyer, makes a speech about retstored "social peace" and says he has full authority from the Polaris Government to restore social peace, and that starts with the shipyards nationalization. GTVA command does not respond for a moment, after that you have to return to base.
2)
Who is in charge in the Polaris system isn't clear anymore. Your command officer is wainting for new orders. The GTVA High Representative is unreachable. The Vasudan Trade and Recovery Office needs you to escort a vasudan convoy to a safer place, Sirius system.
During the mission, the convoy is ordered to power down its engines by NTF fighters because some vasudans aboard are accused of economic crimes under new Neo Terran Workers Protection Act. Half of the confoy powers down, the other will only respond to GTVA authority.
You head to the Sirius node as the NTF fighter turn hostile and try to engage the convoy. The other half of the convoy is destroyed, and your command officer advise you to get out of the system, because if you return to base you will face court martial.
But there is a court martial, and even if you are not convicted of killing "GTVA" pilots, but under Neo Terran Sirius Alliance officers pressure inside local GTVA, you resign and start working for a private military company...
x) Some mission about how Arthur Roemig turned into a SOC operative...
3)
Starting with the player trying to find the Trinity and retrieve a piece of data for the SOC before anyone (NTF, GTVA or Shivans) finds it. You kill Kappa because it spots your AWACS. You find the Trinity and have to persuade Roemig to send the file but he want's to be saved because he feels betrayed by the SOC, but you don't have support to help him, and the Aquitaine recon is closing on you.
Here, you have a choice : use a computer backdoor to extract the data, and feel like a son of a b**** (possibly repell some shivans during the transfer); talk him into beeing a hero ("If you die now, everything you have done for the SOC would have been useless") and lying to him, telling him you gave intelligence to the Aquitaine in order to retrieve the Trinity.
Then you are ordered to retreat to safe distance and call in bombers to wipe out the Trinity, because if the Vasudans learn about some Terrans inside the GTVI working with the NTF, some Vasudan Admirals could turn hostile to the GTVA (ant that happens during the main FS2 campaign in SOC deepcover operations).
The Alpha and Zetta wings shiw up first, and you are ordered to go on with the a fighter sweep, but Shivans show up just at this moment so you can watch the massacre from a safe place, and go home.
4)
A mission (or 2, or 3) a bout taking back home the 4 mara fighters recon emerging from the second knossos. Hiding with a science cruiser inside a debris field, escorting SOC folks to the last destroyer in the nebula, going to the rendez-vous point and finding a whole bunch of shivans and finally, escaping through the node...
5)
A mission about following a Sathanas trough subspace during the Capella event. Some king of Subspace Ops monitoring unknown subspace distorsion, but when everything goes wrong, the only way to survive would be to follow the Shivans to Shivantown. And perhaps finding Bosch. And a whole lot of nebulas. And ancients.