Author's Note: Just a random thought I had.
Gideon was an AI, she was programmed to protect her Captain and to ensure the integrity of the timeline. She would remind anyone who commented that she had emotions that it wasn't possible.
Her seeming affection for her Captain was simply the fact he was who she was programmed to protect. Just because Gideon made sure he was safe, healthy and comfortable beyond the parameters the Time Masters had set, it didn't mean anything. Just because she had defied the Time Masters and gone rogue with him, it was her programming to protect her Captain that meant she followed him. Not because she missed or grieved for those he had lost, who they had both lost.
No, she didn't love or have feelings.
But she hated Agent Gary Green.
Zari had been surprised that Gideon had trapped the Time Bureau agent in the simulation. She had dismissed it at the time. Noting to the woman that she thought it was funny, but Gideon would have happily done it for real.
From the moment she had met the man, Gideon despised him. She hated how cheery he was, how he tried to please everyone and most of all that he was human now.
Gary was no longer an AI for a Timeship, no longer her brother. Instead he had been turned human by an accident that Rip was unwilling to try to recreate for her.
Gideon was still only a disembodied voice while Gary got to have a body.
And she hated him for it.