Between Seasons 8 and 9 of SG-1, following the defeat of the Replicators and downfall of the Goa'uld system lords, she accepts a position as Head of the Stargate Research and Development Program, based in Nevada.

[6] When an advanced lie detector shows they are concealing something in early season 4, it forces Carter and her superior officer, Colonel Jack O'Neill, to admit that they care for one another "a lot more than [they're] supposed to".

Trapped on board the Earth ship Prometheus in season 7's "Grace", Carter realizes that her feelings for O'Neill stop her from exploring other romances.

Shortly after the death of her father in late season 8, Carter breaks up with Pete and goes fishing with Jack, Daniel, and Teal'c to celebrate the defeat of the System Lords.

After Lieutenant Colonel Cameron Mitchell assumes command of SG-1,[9] General O'Neill orders Carter to assist SG-1 on a mission concerning the new Ori threat.

[11] The Atlantis character Dr. Rodney McKay (David Hewlett) has a hallucination of Carter which enables him to survive while trapped in a sinking Puddle Jumper in season 2.

[12] Lieutenant Colonel Carter approaches McKay's sister Jeannie Miller with an offer to work for Stargate Command in season 3.

[13] At an unknown point after the end of the Ori conflict in Stargate SG-1, Carter is promoted to a "full bird" colonel and is transferred to the Midway space station to oversee the final stages of completion.

Carter finds the Atlantis command experience quite relaxed in terms of military protocol, but enjoys it nonetheless ("Midway").

True to her SG-1 heritage, she conducts herself bravely by actively taking part in missions ("Reunion", "Trio") and protecting and defending those under her command ("Be All My Sins Remember'd", "Search and Rescue").

Carter is in command of the George Hammond when it ferries personnel from Earth to Icarus Base to witness the latest attempt to dial the ninth chevron.

The Hammond attempts to fight off the assault on the base by a fleet of Goa'uld ships that Carter presumes belong to the Lucian Alliance.

Although they are unsuccessful in preventing the destruction of the base, they are able to rescue most of the survivors stranded outside, including Colonel David Telford, who was to command the expedition to Destiny.

This includes Jack O'Neill, the Tok'ra Martouf, Dr. Rodney McKay, Fifth, Orlin, Agent Malcolm Barrett, Narim, Pete Shanahan, Dr. Jay Felger, her former fiancé Jonas Hanson, and Joseph Faxon (her duplicitous husband of a possible future in Season 4, episode 16, "2010").

Many of these individuals have (presumably) since died, including: Martouf (and symbiote Lantash); Fifth; Narim; Hanson; and two alternate versions of Jack O'Neill.

When Carter joins the Atlantis expedition as commanding officer, a framed photo of O'Neill is seen on top of a box of her personal effects.

A scene was cut from the Stargate Atlantis season 4 episode "Trio" in which Carter and Dr. Jennifer Keller discuss their love lives.

In episode 12, season 10, Samantha is shot and reveals to Mitchell that she has a file on her laptop with letters to people who she cares for in case she dies.

When Amanda Tapping was on maternity leave at the beginning of season 9, Cameron Mitchell was introduced as the leader of SG-1 who would bring the team back together.

[19] Following negative fan reactions to Carter's cancelled leadership within the team,[20] Ben Browder noted the production difficulties that came with Amanda Tapping's maternity leave, and pointed out that new leaders are brought in routinely into units of the military.

[20] Tapping admitted to also have been "kind of put off" upon learning that someone else would lead SG-1,[19] hoping that the producers would make SG-1 more of an ensemble team in season 10 by removing the patriarchal line of command.

Tapping sat down with Robert C. Cooper at the beginning of Stargate SG-1's season 7 to discuss Carter's struggle with her demons and her life choices in regards to work and family.

"Chimera" is an offshoot of what happened in "Grace", and the writers were trying to "dispel the black widow curse that Carter has, and also to open her up for more experiences and to flesh her out just a little bit more as a human being".

[36] Tory Ireland Mell, reviewer from IGN said that Carter's season four presence on Stargate Atlantis was "underused" and a "slap in the face" to her character.

Many reviewers have felt that Tapping accepted the role of Doctor Helen Magnus to make a name of herself outside the Stargate universe as Samantha Carter.