After several years as Meredith's second-in-command, he was beginning to question the blind loyalty with which he had followed her. Relations between the city's Mages and Templars were growing worse. More and more, the Templars confided their own slips in performance to him, fearing of the punishments that Meredith gave for even minor infractions. While still ill at ease around large groups of mages, he was starting to notice the tension and the fear that filled the eyes of his charges. It was a fear reminiscent of his own and it troubled him. These were the people he'd sworn to protect. Meanwhile, Meredith had become more guarded and evasive when questioned, expecting his devotion.
When the apostate Anders blew up Kirkwall's Chantry, Cullen watched another Circle fall around him. This time the fighting went beyond the Circle, spilling into the streets of Kirkwall. Once again, he fought alongside the Templars in order to regain control. However when Meredith's actions threatened the lives of those around her, he could no longer ignore her actions. Siding with the Champion, Cullen stood against the Knight-Commander.
Stories of Kirkwall's mage rebellion tend to end with the deaths of First Enchanter Orsino and Knight-Commander Meredith - but that was not the end for those living there. Large sections of the city had been physically damaged during the conflict. Beyond that, the people of Kirkwall were angry and frightened. Mages - for years the only threat that Cullen could see - faced the real possibilty of being mobbed by those seeking vengeance. With Meredith gone, the Templars were leaderless and, as he was forced to admit, potentially dangerous. He rallied the Templars to begin repairs on the Gallows and ensure the protection of the loyalists mages who continued to reside within. He coordinated with the city guard, lending aid to relief efforts around the city. For over two years, Cullen effectively lead the Templar Order in Kirkwall, bringing some stability to the struggling city.
Since he had been eight years old, Cullen's life had been a headlong sprint in one direction. It was a course, once set, that could not be altered. Or so he can come to accept.
Seeker Cassandra Pentaghast and Sister Leliana, the Right and Left Hands of the Divine had come to Kirkwall a few years after the rebellion. It was then that Cassandra met Cullen. Impressed by his integrity and what he had accomplished since Meredith's death, Cassandra offered him a position in what would become the Inquisition.
"I do not care where you have faltered - only that you stand here now," she said. "But this is not an order. The choice is yours".
It wasn't long before Cullen once again found himself on the Waking Sea, this time on a ship bound for Ferelden along with Cassandra and her prisoner, Varric Tethras. As Cullen still refused to spend more time below decks than was necessary, Varric often found him staring at the ocean.
"Kirkwall had disappeared by that point," Varric recalled. I asked him if he was ready to leave. He thought for a moment, then said "All of it". I told him that Ferelden might not be better. He said, "I was there during the Blight and the Circle..." and then he actually somewhat smiled. "It can't be worse".
"You know, for a first attempt at optimism, it wasn't bad."