As Dr. Rodney McKay (David Hewlett) struggles to figure out why the stargate has been inoperable for over a week, a mysterious probe plunges into the city. A subsequent decryption sweep of the probe offers McKay a shocking glimpse of nanite code before his diagnostic program crashes and all the data is lost. Meanwhile, Lt. Col. Sheppard (Joe Flanigan), Teyla (Rachel Luttrell) and Ronan (Jason Momoa) have noticed that the some of the crew are behaving oddly. The mystery deepens still further when a former member of the expedition is discovered lying unconscious in a hidden room. Convinced that the replicators have finally found their location, the team grapples with these implications, unaware that their problems may very well be insurmountable.