Cephaus worked under Oberion the Great for many years before the activation of the Halo rings, trying to turn a blind eye to Oberion's wickedness. When Oberion had released the Flood onto his planet and consumed his home, the Plains of Anduu, Cephaus had realized he could no longer let him continue to destroy the lives of others. He felt disgusted that Oberion liked to experiment with the Flood, and sought to bring him down.
After the Forerunners were forced to leave their time, they activated the rings, and began what the Covenant knew as "the Great Journey"; only their source were not the Halo rings. The Forerunners arrived in late 2553, Cephaus heard Oberion speak of humans, their descendants, and how he planned to wipe them out. But Oberion seemed afraid of some of them, whom were rumoured to be "demons". Cephaus decided he could use the demons' help to kill Oberion.
Oberion dedicated the time to rebuild glassed planets, such as Eridanus II and Reach, to house the Flood. When the Dusk arrived at Eridanus II in 2556, Cephaus knew that his chance had come. When he was ordered to attack SPARTAN-116's Pelican, Cephaus (possibly deliberately) fired on Rugari's ship, and took Rugari's shot as well, saving SPARTAN-116 the trouble of doing it. Later, Oberion told him where one of the demons were, and he hurried to find him.
Cephaus was looking over the cryotube of the Master Chief, when SPARTAN-116 confronted him. Cephaus gave no sign of resistance, and willingly waited inside Rugari's captured ship while the Chief was revived. When SPARTAN-116 asked to interrogate him, Cephaus told him everything he needed to know, and offered his help to defeat Oberion.
Cephaus returned to the Dusk with the Spartans, and made some plans with Cortana as to how to defeat Oberion. He decided to tell them about Dr Amelia Dalason and a group of scientists that could help them destroy Eridanus II, and they left to find her.
After realizing Dr Dalason was captured by the Forerunners, Cephaus and the Spartans flew to the Perilous Adytum, where Dr Dalason was being held. They made a fake (and rather funny) fight in the Perilous Adytum, to convince the Forerunners Cephaus was still on their side, and he took the "captive" Spartans to the bridge, as ordered by Commander Vilarius.
At the bridge, Cephaus freed the Spartans, which was made to look like an accident, and he and the Master Chief left to find Dr Dalason. After successfully doing so, he and the Spartans quickly evacuated the Perilous Adytum, which Cephaus set to self-destruct, and hurried to Dr Dalason's laboratory.
Dr Dalason used Cephaus' ship, the Subjugated Phoenix, to power the detonation, but they were ambushed by a group of Flood Oberion left behind. However, Cephaus made it back to the surface without incident.
Oberion was now fleeing in his flagship, the Cessation. As Cephaus returned to the Dusk, the Prowler pursued it to the other built planet.
Cephaus arrived with the others at Reach, and realized that the Elites, a former part of the Covenant, were there. They met up, made a plan to take down the Cessation, and flew down to the remains of Reach, some of which still retained its original agriculture.
The currect Brute Chieftain, Othreus, attacked them with a vast number, but Cephaus, the Spartans, and the Elites fought them off, and waited for Rtas 'Vadum and Commander Lash to attack the Cessation.
After the Forerunner flagship took two NOVA bombs in its middle, it fell to the ground. Cephaus and the Spartans made it to the fortress, only to be apprehended by Oberion's sister Maelia outside of it. Cephaus stayed behind to fight Maelia, while the Spartans hurried inside to find Oberion.
Cephaus had been contacted by SPARTAN-116 prior to the Dusk's arrival. He had made plans to ensure Oberion would be defeated, and constructed a clone of himself to deceive the others into thinking he had died. Cephaus was very grateful towards the Lieutenant Commander for having saved not only his family but several hundred Forerunners as well from the catastrophic event several millenia ago. He then headed to Earth with the rescued Forerunner and UNSC forces.