Before the Hiss Invasion
Rupert Wells is a part of Ranger squad charlie-seven and had a mission to map Quarry grid coordinates G-29 and his second mission was to was to find a route from the Threshold entrance in Maintenance to the Formation, which was not successful. Later on Rupert had a debrief and he talks about the uneventful expedition to the Debriefer, he and Kevin Horowitz both joked about seeing a mermaid to the Debriefer before confirming that there was nothing but rocks.
A Matter of Time
Rupert Wells is found in Containment, Logistics by Director Jesse Faden who was sent by a injured Kevin Horowitz since Wells is a medic. Wells and Jesse fight through the Hiss to get the location of where Horowitz is but they are too late as he is now corrupted by the Hiss. Wells and Jesse both fight and defeat the Hiss corrupted Horowitz, Jesse tells Wells to go to head to the Central Executive in the Executive Sector.