Welcome back, X. True to form, I'm going to disagree.
I don't know... Minerva doesn't show up until well after Genesis is healed and just after he's been already thoroughly defeated, he reaches out to her, and then she vanishes. That looks like rejection, not a gift, and Genesis isn't the one in the position of power, he's just been thoroughly stomped and can barely stand, and long after he has already assumed his WEAPON form and been forced out of it. His strength is already gone by that point, and as soon as she's gone he's not even able to stand. That's not 'I have stolen your power and forced you into to slumber, because he never got to take her hand and has no power. He's already lost his superpowers, he's basically helpless.
The Weapons mostly have materia or gems as part of the design, including Chaos.
The closest similar scene is maybe Cloud in Advent children, where he thinks he's dead and Aeris refuses because he's not done yet.
When Genesis returns healed, Zack says 'you mean... you knew, from the beginning?
Best I've got is this: After S cells are no longer an option, Genesis tries to make himself into a Weapon. People can embody Weapons if they have sufficient physical strength, as shown by Chaos, Omega, and Zirconiade. The difficulty is in keeping you mind in doing so. Vincent and Weiss need the protomateria to control themselves.
Zack shows up and is non hostile. Genesis is also more welcoming than usual. "You're late" implication is that he is expected and... welcome would be too strong, but Zack has a role to play in this.
He starts to transform, and Zack tries to talk to him to help him keep his mind, but fails.
Angeal does something similar in his bossfight, he intentionally loses control of himself by making himself so that he can fight Zack without holding back, as a bonus destroying all of Hollander's samples, and reverts to his human form on defeat.
So the bossfight happens, and Zack destroys the materia, knocking Genesis out of his Weapon Form. But he is healed, so Zack is like 'wait... this was your plan? You knew I'd break you out and halt the process, so you could cheat the planet out of its healing. Wow, that is annoying.' The giant red summon materia is gone because Zack destroyed it.
There doesn't seem to be any reason for healed Genesis to attack Zack, other than being a dick. Angeal had a reason, at least.
Then he's defeated again, and that is when Minerva shows up, in his weakness, not his power. He reaches out, and she doesn't take his hand or get absorbed into him, she closes her eyes and disappears, and the camera pulls out from Genesis looking weirdly sad and giving the impression of falling. Looks like a rejection.
So... best I've got is that Genesis thought he was hijacking the planet to heal himself, but Minerva shows up in his defeat to show him that he had never defeated her, she wasn't forced to heal him, it was a genuine gift. His plan worked because she allowed it to, not because he had power over her. You can't force someone to give you a gift, if you do, it's not a gift.
With the healing and because he's thinking more clearly now, Genesis realises he never had the power, but was given mercy anyway. He is sufficiently touched to sincerely want to help for the first time, but Minerva disappears, not appointing him one of her official weapons. So Gen is left behind, in the knowledge that his plans were worthless from the beginning but that he was healed because the planet chose to, not because it was forced to. Accordingly, he has a change of heart and starts actually wanting to help the planet because it's the right thing to do, not because he was hoping for healing from it anymore
There's a lot of guesswork and jumping to conclusions in that, but it's pretty needlessly cryptic as is, supports a lot of interpretations.
Anecdote I forgot previously. I went into the Behemoth King fight without a build capable of dealing with his regen, so I was about to try the hard way of waiting for her to run out of MP and slowly whittling her down, just to see how long I could last. Then Odin showed up in the DMW and cut her in half.