While delivering a shipment to Fehl Prime in 2185, Messner meets with James Vega and Treeya on a transport en route to the colony's underground research labs. He displays awe and gratitude to Vega for engineering the victory in 2183, making Vega think he is a huge fan, and announces he is proud to be a human. When they arrive, they are barred from entry; security for the labs has recently been tightened, and only authorized personnel are allowed entry. They return to the surface, where Delta Squad is assigned to investigate a strange jamming signal emanating from the outskirts of the Fehl Prime colony. Messner offers to drive them to the location using a M35 Mako he had brought in from off-world from a volus. While he and Delta Squad find and destroy the source of the signal, an alien bio-mechanical device, a Collector ship arrives at the colony and begins harvesting the population. Messner is the one who suggests using the colony defense cannons to take down the Collector ship. After Delta Squad fails to disable the ship owing to a low powered shot, Messner accompanies them to the underground labs to hide.
Inside the labs, Delta Squad learns that the reason the security measures had been upgraded was to keep Messner out; the Alliance had identified him as a Cerberus operative and suspected him of trying to infiltrate the labs to steal research. Messner confirms this, and reveals that he was assigned by his superiors to investigate the disappearing human colony incidents and the Collectors' involvement. Vega is outraged and starts hitting him, but Messner talks him down, arguing that he and Delta Squad now have the same goal: to stop the Collectors. For the time being, they set aside their differences.
When Delta Squad uses a ship piloted by the krogan Brood to break into the Collector ship in order to destroy its drive core, Messner shows his true colors. Before Brood can fire his ship's weapons at the drive core, Messner shoots him multiple times in the head. Without a pilot, the ship crashes and the remaining members of Delta Squad are taken prisoner. Later, Messner explains to Treeya that he had deliberately attracted the Collectors to Fehl Prime using the alien jamming device so that he could observe the Collectors firsthand and learn about their technology and motives. By the sacrificing the colony and temporarily gaining the Collectors' trust, Messner hopes that he will acquire the information necessary to prevent future attacks and stop the Collectors. Messner then takes Treeya to a Prothean archive built into the Collector ship's systems. He had forced two colonists to try and access the archive, but the process had killed them; since Treeya had demonstrated her ability to interface with the Prothean ruins on Fehl Prime, Messner thinks she will be more successful with the archive and forces her to access it. They witness recordings of the Protheans' futile last stand against the Reapers on Fehl Prime, their subsequent transformation into Collectors, and their plan to render humans down into liquified genetic material to create a new Reaper. Messner records this intel on a bracelet, intending to take it to Cerberus.
Before Messner can leave, the Collectors inform him that his usefulness has ended, and prepare a pod for his "ascension" with the other colonists. Messner tries to bargain with the Collectors, threatening to transmit the data he has gathered to the Alliance to use against them, but when the Collectors dismiss his threats and accuse him of bringing the "contaminant" Treeya aboard, Messner grabs her and throws her into the pod reserved for him. She grabs Messner's bracelet while struggling at the last moment. Just as Vega and Essex arrive to rescue Treeya, the pod is ejected out into space to remove the "contaminant". In the ensuing firefight between Delta Squad and the Collectors, Messner fires on Vega, but Vega disarms and stabs him. Vega demands Messner's intel on the Collectors; Messner tries to bribe and begs for his life but James, still angered by Messner's betrayal, refuses the offers. Treeya contacts Vega and tells him that she has the intel and her pod is beginning to enter Fehl Prime's atmosphere. As another wave of Collector drones descend and fire on them, Vega leaves Messner behind to die. Messner continues to beg for Vega's help until a barrage of fire from the Collectors kills him.