When the Cybertronians made contact with the Autobots, Rook expressed confusion about the war his ancestors were fighting, not seeing a distinction between the Autobots and Decepticons. Jhiaxus simply told that they were simply evolutionary throwbacks.
After the encounter with the shadow parasites, Jhiaxus ordered Rook to bomb the parasites.
Rook later fought in the battle between the Autobot-Decepticon Alliance and Jhiaxus's Cybertronian fleet. After Starscream gained control of the Decepticon ship Warworld and turned it against the Cybertronians, and the arrival of the Swarm, Rook contacted his and Jhiaxus's master, the Liege Maximo, to inform them of their increasing problems. Deducing that the situation was getting out of hand, Rook retreated along with the rest of Jhiaxus's crew, save Jhiaxus himself.
Rook later reported to Liege Maximo that they had lost seventeen battalions and that Jhiaxus was presumed deceased. The Liege Maximo told Rook that the battalions destroyed were a mere fraction of his army and that the "day of reckoning" would soon come.