it's one where Mulder and Scully are investigating something(can't remember what) and are separated for a while. Scully goes to this house to question somebody. When the woman opens the door she recognizes Scully immediately. Scully has no idea who she is. The woman brings Scully inside where there are dozens of women claiming to be abductees sitting in the living room. Shortly after they all pull out and hold up vials which have implant chips in them which were pulled out from the back of their necks. that's all the info I have to go on, but if anyone knows thanks in advance.

Memento Mori - Scully's recent failing health is revealed to be inoperable brain cancer which is common among abductees. She meets with other abductees with the same condition and forms a special bond with a dying woman, while Mulder tries to save her from a doctor who may be connected with the abductions.

from season 4.

does this sound like it?

sorry but no. It didn't have Mulder breaking into that facility with the Lone Gunmen.

I just watched Memento Mori last night
The episode Rivero is describing came on before that one. In Memento Mori all the women ended up dead (the last one died in that episode).

Season 3 Mythology 2 parter Nesi/731

Ah the one with the train, thank you!!!