When their commanding officer Jonathan Moran was killed and transformed into a ghost by Albar Prentis, Richard Pritchard took charge against Cass's status. Despite this, she led the crew to the base's Faraday cage, where they would be safe from the ghosts. When the Twelfth Doctor arrived, he hatched a plan to trap the ghosts that involved Lunn leading them to Mason Bennett. However, instead of staying together, the ghost of Pritchard continued to follow Lunn. After cornering his victim, the ghost picked up a wrench, ready to finish Lunn off. Lunn closed his eyes in fear, but the ghost then dropped the wrench and went away.
When the Doctor decided to go back in time before the flood to figure out the mystery of the ghosts, Lunn became trapped with Cass and Clara Oswald behind one of the flood doors. The three then retreated into the dining area, where they caught sight of a ghostly Doctor walking across the lakebed, (TV: Under the Lake) which in fact was a hologram created by the Doctor's sonic sunglasses. (TV: Before the Flood)
After the ghostly Doctor released the other ghosts from the Faraday cage, Lunn, Cass and Clara retreated back there to stay until the crisis had ended. However, after the ghost of Alice O'Donnell took Clara's phone, Clara sent Lunn out to get it. He ended up getting trapped by the ghosts but was released later on.
After the threat was ended, Lunn, Cass and Bennett were the only survivors of the base personnel. Looking in on O'Donnell trapped in the Faraday cage with the other ghosts, Bennett had Lunn translate a message from him to Cass that revealed that Lunn was in love with Cass and how Bennett wished he'd told O'Donnell before she'd died that he loved her. Cass was shocked by Lunn's confession and he quickly apologised before she shocked him by passionately kissing him. (TV: Before the Flood)