The Sam/Jack relationship was fraught with complications, given that he was her commanding officer. Pursuing any sort of relationship would have been inappropriate for both and would only have really been possible late in the series after Jack's retirement. [...] Jack and Sam could have gotten together after Jack's retirement, but it was never made canon because, quite frankly, it wasn't my call. Still, despite the lack of official confirmation, it was only natural that they should get together after the events of Threads and, in my mind, they have been together ever since. An attempt to suggest as much in [Stargate Atlantis'] season 4's Trio, unfortunately, ended up on the cutting room floor when the episode ran long.