When the Doctor opened the Void, sucking in all the daleks and cybermen into the Void, Dalek Sec activated an emergency temporal shift and disappeared.
Dalek Sec appears finally in the Third Series, in a two part story with the Tenth Doctor leading the Cult of Skaro in a bid to recreate the Dalek race in human form. He evolves himself as part of an experiment by engulfing the body of a human. This however leads to him developing compassion and other human feelings. He is betrayed by the Cult of Skaro and killed by them towards the end of the episode Evolution of the Daleks