Special Operations Command (commonly abbreviated to SOC) is related to Galactic Terran-Vasudan Intelligence, though whether it is directly under GTVI command is not made clear. SOC is clearly closely related, and serves as GTVI's combat arm in most circumstances. The Terran portion of SOC played an active role in the conflict with the Neo-Terra Front.
The extent of SOC operations, as befits a group working from the shadows, is not known: SOC was known to be charged with pre-deployment testing of GTVA equipment and provided specialized personnel such as pilots to infiltrate NTF forces. Much effort from GTVI and SOC was focused on the ETAK project, but it is difficult to pin down how much information was actually gathered. Allied Command believed (or said it believed) that the ETAK was some kind of superweapon; yet Allied Command several times apparently allowed ETAK to continue.
It would not be unreasonable to state that in the end SOC had it within their power to have ended the NTF Rebellion at least a week earlier than it actually did, and perhaps kill Aken Bosch in the process or destroy his flagship. However, for unknown reasons, an assault on the Iceni was never considered. When Alpha 1 and Snipes infiltrated an NTF fighter squadron that received orders to protect the Icenifrom incoming asteroids, no order was given from Special Operations to let the rebel flagship be destroyed by incoming asteroids. Instead, it was more important that their activities remained unveiled.
The mysterious ETAK device, believed for some time to be a weapon, was the impetus for Allied Command to infiltrate the NTF via SOC operatives. Alpha 1 of the 242nd Suicide Kings was one of these spies. Once inserted into the NTF, Alpha 1 made contact with Lieutenant Commander Christopher Snipes, the SOC's undercover mission coordinator within the NTF. Once they were established within one of the NTF's fighter squadrons, the first missionundertaken by the pair was to scan the NTF Iceni and acquire any additional data possible, especially about ETAK.
This mission was complicated by the actions of Admiral Ahmose, who, despite knowing the operation being carried out near the Iceni, ordered his Vasudan battle group to launch an assault on the NTF convoy against the orders of Allied Command. His choice threatened the safety of the operation and the lives of the volunteers, and the SOC operatives had no choice but to fire on the GTVA forces, not wanting the Iceni destroyed. The Iceni successfully reached the jump node to Epsilon Pegasi and Admiral Ahmose was branded a traitor and court-martialled.
The next operation did not go as planned, either. The NTF squadron the SOC pilots had infiltrated was ordered to defend an Argo-class transport, the NTT Sunder.
The cargo and destination of this transport was highly classified, which led to the suspicion it had something to do with the ETAK project.
Snipes, with the help of the crew chief of the squadron (also an SOC operative), installed overload devices to destroy the remainder of the squadron. Alpha 1 and Snipes then attempted to hijack the Sunder with the help of a GTVA agent piloting the transport. At this point, secrecy was paramount, and the Alliance deployed their new AWACS, the GTA Charybdis, to jam communications in the area, allowing the operation to remain covert.
NTF fighters responded to a partial message warning of a reactor core breach, and raced to aid the NTT Sunder. Alpha 1 and Snipes, aided by the pilots of an SOC unit, the 99th Skulls, successfully hijacked the NTT Sunder, repelling NTF forces sent to aid in the recovery operation. Blowing up a decoy Argo-class transport, Snipes managed to successfully pin the blame on another NTF commander, who was court-martialled and executed. The NTT Sunder successfully reached the Regulus system and was recovered by GTVA Intelligence.
Snipes was reassigned, and the NTF began to suspect Alpha 1 of being a GTVA operative. Sending Alpha 1 on a suicide mission, they ambushed the fighter pilot and attempted to have him executed in the field. Nevertheless, the 99th Skulls recovered the pilot, as well as sensitive data that had been stashed in the fighter's computers.
Shortly before Capella went supernova, the SOC launched another dangerous mission—using Alpha 1 and three additional pilots to rescue the NTT Grall and Commander Snipes, who had ended up stranded deep in the nebula. He was rescued from a highly electrically-active, Shivan-infested area, along with the crew of his ship.
Alpha 1, Snipes, and two others then volunteered to take part in a mission to infiltrate the area behind the second Knossos subspace portal, which had been discovered by a Vasudan patrol. They flew specially-modified Mara-class fighters, captured earlier by SOC, and modified for Terran use. Behind the portal, they found numerous Sathanas juggernauts, heading towards the portal to the nebula, as well as a large fleet of Shivan cruisers and warships. This expedition's main goal was only to gather intelligence and this succeeded as soon as they gathered information about the true strength of the Shivan fleet.
During the mission, the SOC volunteers inspected and destroyed three Shivan devices of a type never before encountered by the GTVA. Game documentation refers to these devices as Shivan communication devices, or Shivan Comm Nodes, but it is unknown if the GTVA had determined this to be their function by the end of FS2.
After the destruction of these devices, they rushed back to the jump node back to the nebula and were extracted by SOC logistics craft.