Returning to Erioch, the team learns that Galdroon is a deserter, who is being charged for his cowardice. They also learn that another chamber of the Omega Vault has opened, revealing part of a Warp Route chart showing a stable passageway between Arkhas and Atonement. The team is sent to explore the conduit, then recover the Magos Vyakai before returning to Erioch.
At Arkhas, the team must take control of an Imperial voidship that is currently in mutiny, once again using the help of Commissar Falco. They recruit the navigator of this ship to plot their course through the Warp Conduit. Along the way, the discover a previously unknown system that is inhabited by a race of xenos with access to extremely advanced technology. Despite the loss of their Dark Hunter, the team is able to make their escape from the system and finish the journey to Atonement.
On Atonement, they meet Magos Erlan Klute, who convinces them to undertake an operation to destroy a cluster of spore chimneys that would set back the tyrannid invasion of that world, while testing some special gear he has developed to use against the xenos. They succeed in destroying the clutch through the use of a modified cyclonic torpedo. When they return to the base, however, they learn that it was attacked by the Harbinger, apparently using some kind of hybrid Tau/Eldar device to control a group of Genestealers. The purpose of his raid was to steal the rest of the cyclonic torpedo cache kept at Atonement.