First mission: Cerberus base discovered by Council in the Horsehead nebula. Shepard sends out a small away team (may or may not include him) to take out the Cerberus cell. Base is discovered to be larger than previously expected and too much for the small away team. This is the point Jeffery turns, he does something that almost gets the team captured and they escape. They return and are debriefed. Jeffery is now the villain.

Between missions: Jeffery taunts the crew. Shepard being the only knows the truth means he has to put up a façade for everyone.

Second mission: Jeffery and crew of Cerberus (could make named soldiers or just unnamed grunts) attack a lab. Lab contains bioweapon material (makes location important) Shepard’s crew intercepts and fight between crew and Cerberus goes on. One or more of the Normandy crew catch up with Jeffery, but are separated by something that does not allow them to fight and only allows them to talk (this could be bullet proof glass, force field, or anything like that) Jeffery explains why he turned and again taunts the crew as he makes his escape with items he came for.

Between missions: Crew works to find Jeffery and next target. Rallying time for the team.

Third mission: Crew intercepts comms that lead them to the next target. Target is Salarian outpost. Team arrives at same time as Jeffery and battle ensues. Normandy crew is able to push back and forces Jeffery to retreat (win for Normandy crew builds morale) Crew finds out that the outpost specializes in virus research and they are studying the virus that Mordin was thought to have cured on Omega. It was only halted and they come to conclusion that Jeffery wants it.

Between missions: Continue to search for Jeffery. Shepard takes the virus onto Normandy for protection. Scientists on board continue work

Fourth mission (Attack on Normandy): Jeffery, having spent time on Normandy he knows of a weakness in security, leads an attack on Normandy to retrieve virus. Fighting throughout ship, Jeffery makes his way to labs and is only able to retrieve one vial of the virus before Normandy crew is able to get Cerberus off ship.

Between mission: Crew repairs ship and finally gets location of Jeffery. Is on a major Cerberus outpost that was well hidden. Outpost is inside a large asteroid. Shepard prepares attack with crew (this is the location Jeffery was to find for Shepard)

Fifth mission (Final mission): Normandy crew attacks on multiple fronts and enters compound. Fight their way to the war room where Jeffery and a squad of the best soldiers are held up. Also in the war room is a Cerberus general who Jeffery has been working for. Jeffery uses an EMP grenade that disables all weapons and fighting becomes personal. After Shepard and crew kill or incapacitate all soldiers it leaves Jeffery and general. General and Shepard have words back and forth. General tells Jeffery to kill them, Shepard looks at Jeffery and gives some signal which tells Jeffery mission is over. Jeffery takes down general from behind (either killing or capturing)