What if Cloud were the antagonist?
Let's say before the Nibelheim Incident could ever occur, Hojo is instead stupid enough to bring Jenova to the main ShinRa HQ. For argument's sake, let's say Sephiroth stumbled upon this creature by chance.
*
Seeing the name Jenova as the creature's label, Sephiroth begins questioning his existence and doing research. As Hojo is his creator and is here in the building, Sephiroth catches up to Hojo in Shinra's office, he is told the truth of his origins: the fact that he is a perfect specimen, proof of evolution, Hojo's finest achievement, and Shinra's ultimate weapon. Candidly if callously revealing his true intent toward Wutai, Shinra crushes Sephiroth's illusions of heroism (I know, I know, in Crisis Core he already seems aware of Shinra's purpose and doesn't care). He kills the president but Hojo escapes. Sephiroth goes on a rampage to purge the world of these lying blasphemers.
Finally, wrought with guilt over the lives he took for a false cause, Sephiroth vows to do penance, leaving his sword impaled in the president's corpse.
**
Hojo returns and finds Cloud and Zack remarkably alive. He incubates them in Mako and injects them with Jenova cells hoping to create a creature that can defeat Sephiroth. He notes that Jenova has no power over Zack's cells. Cloud meanwhile has become a total wreck. He is so weak, Jenova does not bother to exert its will over him. Curiosity besting logic, Hojo injects Cloud with cells from Zack. The DNA from the three beings intermingles, the Jenova cells now working with Cloud's to absorb and control Zack's. Zack's cells are still too powerful, however, and seem to wield the control instead.
While Hojo is away, Zack and Cloud awaken and smash their way out of incubation. Cloud seems to have no real mind of his own anymore and it is only by Zack's will that he follows him out of the building in the hopes of escaping ShinRa altogether. Zack proves powerful enough to defeat an entire army of ShinRa soldiers sent by Hojo to retrieve him and Cloud. However, Zack's deliberate will over Cloud has wavered and in Jenova's control, Cloud attacks and kills Zack, finally regaining his senses long enough to realize his crime and retreat into the warm embrace of Jenova's raw logic.
Although Cloud's body isn't strong enough to prove a viable weapon for Jenova, she allows just enough of his consciousness to seep through so he can endear himself to others, latching onto his personal understanding that friends can prove a valuable asset. This is the only logical way for Jenova to defeat and absorb Sephiroth who has refused to destroy this planet.
***
Carrying Zack's superior cells, Cloud is now able to grow stronger faster than before. He travels with AVALANCHE to rid the world of Mako reactors. Aerith is able to sense Jenova's will which culminates in her murder by Cloud. He tells the group Shinra was responsible and all continue on their path of righteousness. In Cosmo Canyon they meet Bugenhagen and Nanaki. Cloud agrees to be Bugenhagen's escort during Nanaki's right of passage. After defeating the spirit of Natak, Bugenhagen reveals he knows what Cloud is, resulting in his and Nanaki's deaths. Cloud tells the others they were killed by the Gi. They return to their mission: the final reactor is in Nibelheim. Here, they defeat a small force of ShinRa stationed at the mansion. Cloud encounters Vincent who also seems to know what he is. Vincent is killed and his ability to transform is acquired by Jenova.
****
Cloud's mind begins to surface in this town. His emotions for his family and for Tifa beginning to force out Jenova's will. Jenova's last desperate act to regain control forces Cloud to slaughter the town, razing it in flames. Finally seeing Cloud for the murderer he is, Cloud's group confronts him, but he is too strong now for them to defeat him alone. Biggs, Jessie, and Wedge are killed in the conflict.
Despite knowing they can't survive another confrontation, Barret and Tifa pursue Cloud past the cliffs of Nibel. In Rocket Town, they find the town in ruins with a few ShinRa soldier's bodies mixed in amongst the carnage. Barret and Tifa find Cid who is barely alive. There are other people in town who are better off and are able to help. They tell that Rufus Shinra and Hojo had arrived asking for Cid's plane hoping to get to some "promised land" up north. But the First Class (Cloud) arrived and rained havoc. Cid recovers and, having watched Cloud murder Shera, agrees to take Barret and Tifa to Wutai where Cloud was last seen headed.
*****
Wutai is the place of the final "first disc" confrontation. Wutai is where Sephiroth has made his home having hermited himself in Da-Chao. The group arrives in time to see the end of a battle between Cloud and Sephiroth in which they each leave the other weakened. Before Cloud can deliver the final blow, the group intervenes. Suffering defeat at the hands of mortals, Cloud admits he is not yet strong enough and flees. Sephiroth admits a passing recognition of Cloud but more deeply realizes he is corrupted by Jenova to which he shares a fundamental link. He also shares that he has been having horrible visions of mayhem and the group surmises this must have been due to Cloud's actions. Despite this and Cloud's imminent threat, Sephiroth refuses to return to war as his penance is not yet complete and may never be.
"DISC TWO"
With that ridiculous cop out said and done, the group leaves returning to Junon where what remains of ShinRa is currently stationed including Rufus. Here they confront Rufus about the promised land and its relation to Jenova. While Rufus knows nothing about Jenova, he explains that the promised land is his ticket to world domination as possessing it will grant him utter monopoly over all the world's energy. The group wonders if he hasn't got that already. The group then harasses Hojo who explains that the promised land is located in the center of a crater up north where the original body of Jenova was discovered. They wonder if Cloud is "returning home" and try to find a way to reach the crater.
Meanwhile, Reno and Rude arrive having barely survived an attack on Gold Saucer where a mysterious First Class SOLDIER murdered everyone and stole a green stone. No one knows the significance of the stone unfortunately. However, Cid has managed to get the company's first airship, the Highwind, up and running and despite the friction between the two parties, the trio agrees to go with Rufus and Hojo to the crater. Before they can leave, Sephiroth arrives and agrees to the accompany the group just this one time. Mid-flight, Hojo explains that Cloud is a Sephiroth-like creature: a curious statement as for what they know, Sephiroth doesn't seem to be insane. Nevertheless, only Sephiroth can defeat Cloud and vice versa.
******
They arrive in time to witness Cloud's descent into the crater. Confronting him, they learn he plans to absorb the planet by controlling the lifestream. But first, he has to create a catastrophe similar to Jenova's arrival on the planet. He produces the black materia with which he would summon meteor. The group is able to defeat Cloud due to Sephiroth's help, but Cloud has learned a new trick. He invades the mind of a Jenova-injected SOLDIER who tosses the fallen black materia to Cloud as he plunges into the lifestream in the massive chasm beneath the crater. Although the soldier tries to attack them, Sephiroth is able to subdue him through will alone.
Rumbling stirs them to retreat and they watch as several daikaiju emerge from the crater. Looking up, the group sees the colossal meteor looming in the sky. More concerned with press than with resolution, Rufus suggests executing AVALANCHE for causing all of this. Sephiroth disagrees and proves it impossible to go against him. Cid suggests there may be a way to blast that thing out of the sky if he can his rocket up and running. Scarlet is all gung-ho on the idea but explains that a single rocket won't possess enough power on its own. She goes on to suggest they gather materia; the bigger the better. The group then obtains samples of large materia from Junon, Fort Condor, North Corel, and Midgar. Knowing ShinRa will never reopen their space program, Cid demands to pilot the rocket in a kamikaze run. He doesn't take no for an answer. The group joins him as the rocket takes off which pisses him off 'cause who the hell's gonna stop Cloud now? Once they've left the planet's atmosphere, the group discovers an escape pod built into the rocket by Shera. Though Cid gets hyperemotional over this discovery, the group manages to escape just before the rocket smashes into Meteor.
*******
On their return, the group finds those daikaiju wreaking havoc on the towns. Using the Highwind, the group manages to defeat Ultima. The Junon cannon has been used to great effectiveness against a sea dwelling daikaiju and has since been moved to Midgar to blast a hole in a barrier that has appeared around the crater. A single shot manages to defeat another daikaiju and destroy the barrier. The monsters gone and having no other way to stop Meteor, the group travels deep into the crater where they're sure to find Cloud waiting at the center.
Again, due to aid from Sephiroth, the battle is won. But Tifa's battle for Cloud's soul has just begun. As the others escape, Tifa dives deep into the lifestream to seek out Cloud's consciousness.
Barret, Cid, and Sephiroth realize there is no way to stop Meteor. Although the planet won't be destroyed, all life will be wiped out.
In a world resembling Nibelheim, Tifa finds a boy. Young Cloud is frightened and distraught. He thinks there is a way to save everyone but he can't find it. Tifa takes Cloud through his subconscious and they eventually encounter Aerith. She's not just a memory though. Her consciousness has linked with Cloud's. She explains that she had been trying to stop Cloud and even trying to summon a force that would counter Meteor but Cloud was holding her back. The key to the world's survival now is for Cloud to let go. Unwilling to let him go, Tifa surrenders to the lifestream so they can be together.
Everyone on the planet is shocked to witness a massive force unleash from the planet's surface and force back and destroy meteor. Everyone celebrates except Barret, Cid, and Sephiroth who take a moment to consider Tifa's final act.
Barret returns to Kalm where Aerith's mother had agreed to keep his daughter. Cid joins ShinRa on promise they'll look into restarting the space program. Sephiroth returns to his life of solitude.
Did I miss anything?
