Stargate Atlantis and the actress behind Dr. Elizabeth Weir seem to have gone their separate ways.

The actress has turned down an offer to appear in an episode of the show’s fifth season, which the writers hoped would be the start of an on-going arc, according to executive producer Joseph Mallozzi.

After three years in the role of Atlantis’s civilian commander, Torri Higginson was reduced from regular cast member to recurring status, appearing in four episodes of Season Four. Weir suffered a close call with a Replicator energy weapon, brain surgery, and captivity and cloning at the hands of the Replicators.

Just when fans thought the character had been killed off, Weir returned for the shocking final minute of January’s top-rated episode “Be All My Sins Remember’d.” Elizabeth, or perhaps some form of Replicator copy of her, was in command of a group of surviving Replicators who are about to undertake a secret project, now that Oberoth and the rest of the Replicators have been destroyed.

“Last year, after we shot that final surprise scene in [“Be All My Sins Remember’d”], I stopped by Torri’s trailer to congratulate her on a job well done and, also, to assure her that the door was left wide open for Weir’s possible return (in some form, be it repli-Weir or other) the following season,” Mallozzi said Friday in a post at his blog. “Torri was excited by the prospect and, in particular, had great things to say about her new leather outfit.”

The writers had devised a new storyline for Higginson’s character, which they planned to revisit in Season Five.

“As Season Four wrapped, Carl [Binder] and Paul [Mullie] got to spinning and came up with a terrific storyline that picked up where that last scene of [“Be All My Sins Remember’d”] left off,” Mallozzi said. “We had a story in place for one episode, the starting point of a potentially bigger arc. The script was written and we eventually contacted Torri who, after much consideration, turned down the offer to reprise the role of Elizabeth Weir for the episode.

Weir shocked viewers with her reappearance at the end of “Be All My Sins Remember’d,” indicating the the show’s writers still had plans for her.

“We are, of course, disappointed, but nevertheless respect Torri’s decision and wish her all the best in her future endeavors.”

Higginson’s reasons for turning down the job are, of course, unknown. But the relationship between the actress and the studio has been understandably strained since the actress — who signed a 6-year deal and relocated to Vancouver when she was cast in 2004 — was removed from the cast list.

“The very last day of filming Season Three, as I finished filming the last scene on the last day, I was called up to the office and was told that my character was going to become recurring if I chose to be,” Higginson recently said in an interview with DTRN’s “SciFi Guys” Internet radio program. “So, I thought that was not a very dignified way to deal with it, and I was a bit surprised. So my reaction was — I was a little bit surprised. I was a little bit upset by how it was dealt with.”

The producers, for their part, believed they were being gracious to Higginson. “Do you know how many actors find out their role on a show has been diminished or done away with?” Mallozzi wrote on his blog, in response to a fan question about Higginson’s comments. “The season wraps, the actor leaves for hiatus, and then his or her contract isn’t picked up. Their agent does the math for them. To many producers, this a much easier and less confrontational way of handling the situation which, obviously, lacks the professional courtesy and respect of a face-to-face meeting.”

Whether the writers still plan to revisit the rogue Replicator storyline — sans Weir — remains to be seen.

As for Higginson, she has guest starred in a recent episode of N.C.I.S. and will appear in two forthcoming films: “Yumi in Love” and “Smile of April.” Visit the fan Web site Torri Higginson Info to learn more.

Season Five is now in pre-production, and goes before cameras next week. Season Four is now airing Fridays at 10 p.m. (9 Central) on SCI FI Channel in the United States.