"Five years after the Nibelheim Incident Sephiroth puts his plans into action by taking control of Jenova's main body in Shinra Headquarters, morphing it into a vessel in his likeness, murdering soldiers until reaching the top of the building and impaling President Shinra. From there, Jenova escapes into the outside world. Cloud and his party chase "Sephiroth" across the Planet unaware it is Jenova under Sephiroth's control. Cloud follows Sephiroth to exact revenge for Nibelheim's torching, but on subconscious level is being guided by the Jenova cells inside him, as unbeknown to him he is also a "Sephiroth Clone," albeit considered a failed one by Hojo. Several times throughout the party's journey the cells make him mentally unstable, and Sephiroth ultimately exerts his control over Cloud to make him hand over the Black Materia.
As the party follows "Sephiroth's" trail they run into pieces of Jenova he uses to hinder their pursuit and to keep them from discovering the truth. The first piece encountered, described as Jenova's arm, transforms into Jenova∙BIRTH and is fought on the cargo ship. Jenova∙LIFE manifests as Sephiroth when he murders the last Cetra, Aeris Gainsborough, at the altar in the Forgotten Capital. A third battle with Jenova occurs in the Whirlwind Maze with Jenova∙DEATH.
As Cloud and his friends defeat the last of Jenova's original body Cloud realizes that what they had been pursuing wasn't the real Sephiroth. The party finds Sephiroth crystallized in hibernation and under his control, Cloud relinquishes the Black Materia, allowing Sephiroth to summon Meteor. Sephiroth's plan is to wound the Planet so greatly the Lifestream would be summoned to heal the area allowing him to absorb it and become a god-like being.
Cloud recovers and throws off Sephiroth's influence and together with his party descends into the Northern Cave to defeat him. Before the final battle they fight Jenova∙SYNTHESIS, a form of Jenova composed of its remaining cells—this form is considered the creature's true form. Once it is defeated the party reaches an evolved Sephiroth and defeats him."
At the start of the game when you reach the broken container in the Shinra HQ someone in your party says that it seems that the container has been broken from the inside out. So it couldnt have been Sephiroth stealing Jenova. It broke itself out. So at that early point the game already gives you a big hint.
''Hadouken!''
