A Russian officer arrives at the SGC with an apparent infectious virus. However, the SGC is put into lock down after they discover that the Russian Officer does not really have a virus after all, but is inhabited by the remains of the SGC's old nemesis ? Anubis.

The Mafia and the FBI both pressure Monk into taking on the case of five mobsters gunned down in a barbershop.

Al's body has been transmuted into a bomb by Kimblee just before his death, and Scar, in a fit of compassion, prepares Al to be saved by turning him into the Philosopher's Stone. Scar sacrifices his right arm, melding it with Al, and making Al a container waiting for the army's invasion of the city. Ed manages to fight off the two homunculi and with Ryla and Rose, they escape, but Ed knows he has to go back, and returns to the city. Mustang, using information gathered by Armstrong in his mock service of Archer, goes down to Tucker's research room to put a stop to the madness. They are beset by chimeras and though they have little trouble fighting them off, Archer gets away. Before anyone can stop him, he sends the army into Lior. There Scar sacrifices himself to transmute the army into Al's body, making him the Philosopher's Stone.

At the brink of another civil war, Scar justifies his intentions for Lior to Ed. However, after learning from Lyra what Scar intends to do to the Military, he sends an urgent message to Mustang to stay out of the city. Meanwhile, back at Regional Headquarters, Al ponders Martel's warning as the Military gets ready for battle.

An alien intruder has found its way into the city, threatening the security of the base. Dr. McKay's experiments with alien technology land him in trouble.

New technician Nina Farr arrives on the job but riles Comfort up the wrong way straight away. Things take a worse turn when she's called to a shout - not knowing that it's her boss Josh whose ceiling has caved in after leaving the bath on - and treats Josh with little respect. Will Nina be able to get past her terrible first day? Meanwhile Josh's date with Caroline doesn't go as planned and Lara takes desperate measures to make sure Harry doesn't accept Simon's resignation.