Appearing at the London Film and Comic Con on 2 July 2006 John Barrowman confirmed that Captain Jack would be appearing in the third series of Doctor Who.
John is quoted on his official site as saying:
“I’m not in series 2, because they didn’t want to put me up against David. They wanted him to be able to establish his Doctor.
They felt Captain Jack was too much of a powerfully strong character that it might take away from his glory. Shucks! So yeah, David has established himself now, but Jack will be back in series 3 and I promise you that because I’ve already signed the contract!”
The full transcript can be read by following this link.