Like alex-ross77 this episode wasn't clear to me on first viewing. But after seeing the episode again recently it made more sense to me.
The brain disease Mulder had was caused by the alien "black ink" virus that was the ultimate alien invader of the series. Mulder became infected but was somehow able to hold out longer than anyone else had done even though he was dying. At one point the CSM commented on the irony that in advocating keeping Mulder alive all these years he (CSM) had found the one person who could be the basis for a race of humans able to withstand the virus. The scenes in the lab are of the CSM somehow transferring the immunity to himself with the hope of eventually transferring it to the others in his conspiracy.
I don't think Mulder was ever spirited away to some suburban dreamland, but instead was kidnapped directly from the hospital to the lab by the CSM. It was clear from comments made by the CSM to Agent Diana Fowley in the lab that Mulder was dreaming all this up while his brain was fighting off the infection. Ultimately it reflected Mulder's wish to have the burden of the X-Files lifted from him.
The brain disease Mulder had was caused by the alien "black ink" virus that was the ultimate alien invader of the series. Mulder became infected but was somehow able to hold out longer than anyone else had done even though he was dying. At one point the CSM commented on the irony that in advocating keeping Mulder alive all these years he (CSM) had found the one person who could be the basis for a race of humans able to withstand the virus. The scenes in the lab are of the CSM somehow transferring the immunity to himself with the hope of eventually transferring it to the others in his conspiracy.
I don't think Mulder was ever spirited away to some suburban dreamland, but instead was kidnapped directly from the hospital to the lab by the CSM. It was clear from comments made by the CSM to Agent Diana Fowley in the lab that Mulder was dreaming all this up while his brain was fighting off the infection. Ultimately it reflected Mulder's wish to have the burden of the X-Files lifted from him.