Synopsis
In the present Gamora is on Halfworld looking after a young Magus, but she leaves him temporarily to confront the 'ghost' of Thanos who's watching them. (She killed Thanos in Infinity Wars Prime and this ghost may just be in her head/conscience.) And she continues to reminisce to *him* about their early life together.
Back in the ongoing flashback they are on the Kyln facility at the edge of the universe. Very young Gamora is attacking him with Proxima Midnight's 'pitchfork' but of course the Titan shrugs it off. Death appears to them and mocks him for coming here to let the anti-matter of the Crunch kill him. He protests that that *wasn't* his plan and she *isn't* Death - who reveals herself to be Magus in disguise.
Magus says that he knows enough of the future (because he comes from the far future) to know that the 3 of them are destined to fight. In fact he seems to claim that he engineered their original meeting (and that he's been impersonating Death from that point in #1). His purpose in getting the 3 of them here is to persuade Thanos and/or Gamora to join him. He holds the Titan back with a forcefield while he gives the girl the usual offer of convert (to his Universal Church Of Truth) or die. She rejects him so he threatens her life to get Thanos to submit.
Back on Thanos' base Zero Sanctuary many of the crew are mutinying and fighting against others. Ebony Maw and Proxima Midnight of the elite Butcher Squadron thread their way through the conflict back to Thanos' control room to try to figure out what their boss's plan must be. They discover that the orbital station is surrounded by warships of the Universal Church and that Sanctuary has started moving to ram their command ship. They commandeer an escape pod and get out before the 2 ships collide. The Blood Brothers seem to be the only other survivors in another pod.
Magus feels the death of so many of his followers which temporarily weakens him. *This* was Thanos' plan, although he seems to think he's killed *all* Magus' flock. Whatever, it will take Magus time to rebuild his strength. So for now he just beats the 'god' up to emphasise how easily he can be defeated. And then he restrains Gamora from killing Magus, saying that she'll do it some day in the future while he watches. They leave Magus on Kyln, but Gamora doesn't understand why he didn't just let her kill their foe then. (Present-day Gamora thinks it was because complicated Thanos didn't want to completely ruin the little girl's innocence yet.)
Many months later Sanctuary 1 is under construction. Ebony, Proxima and the BB's come begging Thanos' forgiveness for the things they did in earlier issues. The Titan actually commends the 1st 2 for their smartness in betraying him when he seemed weak and being survivors. So he promotes them to his new Cull Obsidian, which seems to include young Gamora. (And we know that the Blood Brothers are still working for him in his 1st published app in Iron Man #55.) A later scene shows young adult bladeswoman Gamora with her cybernetic arm and leg replaced by vat-grown limbs indistinguishable from the real thing. And another scene shows her with Thanos as the most dangerous woman in the galaxy in her original (Strange Tales #180) green outfit.
In the present the reincarnated young Magus asks Gamora if she ever really saw Death. She says she thinks it was Magus all the time (and presumably it was his plan that Thanos would be drawn to her because she seemed to be the only other person who could see his love Death). Now she tells young Magus to take her small spaceship Lachesis/Lucky and go find his new destiny in the universe. But in case of need she's programmed in a destination he can choose where people who've been hurt by Magus go.
She's left on Halfworld with Thanos' ghost who questions her decision. She says that if the young boy is to have a chance of growing up good he needs not to be raised by a killer like her, as she was raised by Thanos.