First things first, it appears the true mission of the Spec Ops is to retrieve William Birkin and escort him out of the city into government custody. However, they are advised by their CO to not reveal this information to anyone, so when they encounter Jill and she asks them what they're doing there, they tell her that their mission is to rescue survivors and collect evidence implicating Umbrella in the outbreak.

After meeting Jill and, presumably, fending off Nemesis, the team heads to City Hall, believing that it will offer clues and information regarding Umbrella's involvement. While there, they discover video footage of the USS, alerting the Spec Ops to the opposition. Whether the footage is of Wolfpack or the generic USS grunts you will likely be facing during the campaign is unknown. They also find plans that disclose the location of Umbrella's underground laboratory, and their CO orders them to infiltrate the lab via the sewers.

Somewhere along the way, possibly in the sewers, the Spec Ops run into Claire, and she asks them to help her find Sherry, who has gone missing. The CO says finding Sherry might ultimately aid the team in locating and extracting William, because they have not heard from him since before the outbreak. Once Sherry is located and reunited with Claire, another team of Spec Ops escort them outside of the city (I would wager specifically the train yard from the final USS mission).

The Spec Ops arrive at the underground laboratory but must ultimately destroy it (or a part of it) to contain a threat they encounter (possibly Birkin?). They are then contacted by their CO, informing them that all contact has been lost with the team that was escorting Claire and Sherry, and they need to head to their last known coordinates to protect them, as well as Leon, from the USS. This seems to be the final battle from the USS campaign, but this time you're protecting Leon, Claire, and Sherry from the USS and aren't given an option to save or kill them. Afterwards, the trio are taken into protective custody.

After this, there is one last mission for the Spec Ops. They are ordered to move to the Dead Factory (the P12-A factory from the USS campaign), and it is here where you will get to play through the battle between the Spec Ops and T-103s, the aftermath of which Jill witnesses at the end of RE3. You will be faced with several T-103s, and you will have to utilize the Paracelsus' Sword rail cannon to defeat all of them. One player will operate the cannon, while the other players will have to fend off the T-103s as well as operate the various levers and switches which power the cannon.

This is apparently where the mission ends.

don't find out what happens to Jill and Carlos.