Richard T. Jones in an interview with TVadict.com has cast further light on what his character Ellison will be going through in season 2 of Terminator: the Sarah Connor Chronicles. (spoilers)

Jones said of his characters arc in season two, "after the big incident at the end of the season finale, Ellison is essentially fired. Well, asked to take a leave of absence far far away. I quickly get a call from Shirley Manson’s character and start working for her and this big Corporation...
Ellison’s job is to investigate certain ‘incidents.’ So I go out there looking for things that can really help me find Cromartie. Who I’d like to bring to justice because of what he did to all my FBI friends."

Jones went on to say that while he hasn't seen any scenes yet where he finally speaks to Sarah Connor, it was going to happen.

Source
TV Addict Ellison Interview