In S03E08 "Twilight" Archer became infected with the parasites which kept him away from his duties due to long term memory loss. I think it's safe to assume that the Xindi still went back in time to 2004 to build the bioweapon to destroy humanity like in the events of S03E11 "Carpenter Street". If Archer wasn't involved in stopping the Xindi bioweapon, how were they stopped?
I could only imagine the dramatic tension created when Archer struggles with space alzheimers and forgets he went back in time 150 years to stop space lizards from releasing the space flu. Oh my.
It could have been an interesting two parter. Part I Archer gets infected and goes back in time with Daniels and T'Pol. Part II, T'Pol and Daniels search for Archer and the weapon kind of like Kirk and Spock searching for McCoy in "City on the Edge of Forever".