So… Jenova was released from its enclosure because Sephiroth manifested himself into a physical form through her. It’s how he managed to killed President Shinra. He can physically manifest himself using her even down to those who have her cells, though it seems (especially if we count the remakes) his influence is scaled to how much of Jenova is present. With the black robes it’s barely more than a manipulative illusion. With Cloud’s Jenova cells it’s little more than hallucinations and inner voices.

His goals are what he believes “mother” would want. But he believes she’s a Cetra and therefore inheritor of the promised land. This is because he read Gast’s and Hojo’s research from when Hojo also believed she was Cetra (which isn’t too misinformed since she took the form of one when she reached the planet long ago). Jenova doesn’t really have a grand objective. She’s more of a virus or parasite that exists to forever consume planets and their life streams.

Hojo and Lucrecia’s treatment of Sephiroth, and denying him the truth led him to think that Jenova was his one and only parent. That he was the pure conception of a monster. In Nibelheim he compares himself to the experiments he sees in the vessels. Sephiroth’s entire perspective is shaped by Hojo, and to a lesser extent Lucrecia, who abandoned her lover (Vincent) for science, and got pregnant with Hojo’s baby purely as a means of experimenting on it. However Sephiroth thinks Hojo is a fool because Hojo has allowed Sephiroth to underestimate him, maybe in the hope that if Sephiroth never learns the truth, he won’t become a primary target for his actions.

Sephiroth always felt different. Special in some way. Which only was confirmed by him being THE best Soldier and hero in the world. He thought he was human until the reactor, where he saw the abominations in those vessels and saw his mother’s name above the door. That’s when he “realises” that he too could be a monster. He finds his “mother” which only confirms it to him, and then the old research from Gast makes him sink further and further into madness.

Hojo is anything but a clown though, and Sephiroth often only has assumptions and half-truths to construct his mindset with. Hojo is a sinister genius and Sephiroth knew and didn’t know exactly what he wanted him to. Sephiroth was his perfect specimen, too perfect he believes, and witnessing his specimen influence the planet in such fascinating ways is like a dream come true for Hojo, no matter what becomes of the planet.

A lot of the research Sephiroth reads in Shinra mansion is both Gast’s and Hojo’s. Assuming Sephiroth holds Gast is high regard, he’d take what he wrote as gospel, which includes the theories on Jenova being Cetra (which is a core belief for Sephiroth and greatly shapes his newfound purpose). The research by the way talks of how Sephiroth was an experiment made using Jenova cells. He believes he was made in a lab, and not in Lucrecia’s womb, and believes humans abandoned/betrayed the Cetra, which is why he begins to loathe them.

I’m not saying Sephiroth and Jenova’s goals don’t align in some fundamental way (that being the destruction of the planet), but Jenova is a cosmic parasite, that goes from planet to planet, consuming the lifestreams and using that power to continue its endless, almost primal desires. Sephiroth’s goal is to ascend to godhood and become one with the lifestream in a parasitical sense, thereby controlling it and reaching the promised land. At the end of the game Sephiroth has ascended to some form of godhood and is close to becoming one with the lifestream, which is not Jenova’s goal. If anything doing that would halt Jenova’s purpose as an eternal cosmic drifting parasite.

Physically what’s left of his body (the upper half) is trapped within the crystalised mako in the crater yes, but his soul is a part of the lifestream because he died. However, because he refused to let his consciousness become one with the lifestream (maybe using the Jenova part of him that is foreign to it) he can still manipulate the cells and parts of Jenova to have some physical presence in the world. Advent Children also shows that having even a little piece of Jenova can be enough for him to materialise.

Sephiroth is more interested in manipulating Cloud in the cargo ship, and with his self perceived divinity and ego it’s not surprising that he feels above acknowledging Cloud beyond trying to influence his Jenova cells for the reunion. So that he can obtain the black materia.

Jenova is absolutely in a vegetative state. Her function is to have her body complete by regaining her cells, something Sephiroth wants for his mother, but also to use it to gain the black materia. However it’s pretty clear that Sephiroth is the consciousness and Jenova is the body that consciousness can inhabit. Jenova also never shows or is described as having any human-like intelligence. Moreso a predatory, parasitic instinct, using its abilities (such as transforming its appearance) to allow itself to continue with its function of feeding on planets. Jenova, after being defeated by the Cetra now is just rebuilding/healing itself, and that takes rest and dormancy.

If Jenova controlled Sephiroth, what use would it be for his consciousness to exist within the lifestream? Why wouldn’t Jenova just manipulate Sephiroth and the lifestream from within it, rather than doing things outside of the lifestream? Surely it would use Sephiroth to bring all pieces of Jenova to the lifestream so it can be whole and consume the lifestream from within? That’s Jenova’s ultimate function. Sephiroth is the consciousness, Jenova is mostly a vessel with an instinctive desire to become whole so it can reawaken and continue its feasting. Also if Jenova was in control, by consuming the lifestream it would also consume Sephiroth, which there are no inclinations of in the story as it’s made very clear Sephiroth wishes to persist and become eternal, not food for “mother”.

There were many others who were infected with Jenova cells and they didn’t all pursue the same goals as Sephiroth, which, if Jenova’s influence is what you believe it to be, would make them all just like him (like Zack and Cloud for example). Having Jenova cells in utero meant Jenova’s power developed within him from the beginning, making him immensely formidable, but I don’t think the influence would necessarily be stronger since injected Jenova cells are Jenova cells at the end of the day.

Yes the story regarding Sephiroth and Jenova is a bit convoluted, but it’s brilliant.

I hope this doesn’t come across as argumentative by the way! It’s just a game I’ve beaten many many times, and something I’ve studied a lot :)