"Cole and Railly break into the Night Room, only to find that the Army of the 12 Monkeys has gotten there first, having gotten its location from Jennifer Goines. The Pallid Man tortures Cole to learn how to break into the Night Room's vault, revealing to Railly that Cole had killed Henri; however, Cole does not know how to open the vault. Later, Cole explains to Railly why he killed Henri and reveals more of his past to her. In 2043, prompted by Max, a suspicious Ramse rifles through Jones' personal belongings and discovers that she had sent other chrononauts into the past besides Cole in order to perfect the time-travel protocol, some of whom had died in the process. Ramse confronts Jones, but grudgingly agrees to go along with her for the time being after she promises to protect Cole. In 2015, the Army manages to open the vault door, revealing the source of the plague virus: a centuries-old preserved human torso. The Pallid Man tricks Jennifer into deactivating the final failsafe protecting the vault, but Cole and Railly activate the Night Room's safety mechanism, which incinerates the viral specimen. Railly is captured by the Army and Cole splinters, leaving Jennifer alone. Back in 2043, Cole finds himself in what appears to be an alternate future where the West 7 have taken over the time machine facility."
So it seems apparent to me that the cause of the virus, the human remains, are actually because of the the time machine in the future. I think those remains are from an immune carrier from the future who was sent back thereby starting the virus itself. Seems like a huge paradox, but that is what it looks like right now. I also think those remains where Coles remains. I think that because of the reaction he had both times he got near them, it was similar to when the two same watches from different times lines got near each other. Plus, Jennifer made a comment about there being "something about the eyes" of the remains. I've only ever heard her talk about Coles eyes before.
