The experienced and highly decorated Colonel Dimitri Karpov has arrived from Russia to join the Stargate programme, for which he’s volunteered. He has a meeting with General O’Neill about his assignment and naturally requests leadership of SG-1. Jack isn’t interested in hearing what Karpov wants, least of all his desire to grab the job everyone on base wants, and dismisses him quickly.
Daniel, Teal’c and Carter are in Carter’s lab when Jack joins them and mentions his encounter with Karpov. Daniel reminds Jack that they haven’t really fulfilled the promises they made to the Russians in the past, a reference to the events of 48 Hours and the deal Daniel brokered, perhaps. They also discuss leaving SG-1 a three-man team. Carter mentions there is nothing in the regulations saying it needs to be a four-man team and Jack is relieved at one less decision to make. Just like that, the decision is made. SG-1 is a three-man team.

Karpov is alone in his quarters, quite unwell, and we see lesions on his arms. Daniel then goes to visit Karpov to welcome him and smooth things over after the Russian’s run-in with Jack. He asks him not to take it personally and tries to explain Jack to him and also the fact that as Jack is newly appointed to command of the SGC, this is not a good time to pressure him.   Then Karpov collapses dramatically and Daniel tries to catch him. Karpov’s condition is quite serious according to new character Dr. Smith, apparently some form of contagion which results in Jack puttingthe base on lockdown and ordering all off-world teams to go to the Alpha Site.

Spoilers are quite confusing for this episode as there are references both to Daniel seemingly being infected with Karpov’s illness *and* being shot and losing a lot of blood.

Meanwhile, Karpov is not responding well to Smith’s treatment and his prognosis is poor. Karpov is in isolation, worried for Daniel and apologising to Teal’c for Daniel’s condition. It’s through this conversation that we learn Karpov has lost some of his memories and is also experiencing strange flashbacks and dreams.

Daniel himself bears no ill-will over what has happened to him and shares a touching scene with Karpov in which he urges the Russian to keep on hoping when the man would’ve given up, asking Daniel to get a letter to his sister.

In reference to his illness/injury,although Daniel is about to be discharged from the Infirmary, he’s using a cane and also has Teal’c as his wheelchair chauffeur.
There are indications that a Goa’uld is jumping hosts within the SGC, starting out in Karpov, then perhaps moving on to Daniel and from him to another host. Daniel too experiences a flashback and realises something is seriously amiss. Spoilers are far from complete but it appears SG-1 take action against the threat of a possible Goa’uld infestation, including Daniel. The action picks up when the Stargate is remotely activated and Carter tries to override it.