When the dæmons were let out of their cages during the fire drill, it fell to Dr Cooper to explain what had happened to Marisa Coulter. He also told her about the developments that had been made in the intercision process.
After the attack on Bolvangar, Dr Cooper was taken prisoner by the Consistorial Court of Discipline. He was initially kept in a room with nothing more than a chair, bed and bucket. One day he spoke directly to the Father President of the CCD, Hugh MacPhail. As a result, he was granted better quarters so that he could recall and rediscover the research of an old colleague from Bolvangar who had theorized about how to harness the power of intercision like Lord Asriel had done to create a bridge to another world.