The North Crater was created when the asteroid or meteorite that contained Jenova crashed into the Planet thousands of years ago. Jenova began to destroy the Planet's lifeforms until the Cetra sealed her within the crater. The Planet placed its guardians, the Weapons, to lie in the crater in case another threat as great as Jenova would appear. Jenova was left dormant until Gast Faremis, working for Shinra Electric Power Company, unearthed her, thinking Jenova to be an Ancient.

Later, when Sephiroth was defeated by Cloud Strife at the Nibelheim Mako Reactor during the Nibelheim Incident, he traveled through the Lifestream to the Northern Cave to recuperate. Five years later, Sephiroth, controlling Jenova and making her use his form, leads the Sephiroth Clones to the crater.

Cloud and his party follow Sephiroth north after the events of the Forgotten City. The party travels through the Great Glacier and are confronted by Gaea's Cliff. After conversing with Mr. Holzoff, a climber who never reached the cliff's peak, they climb up and discover the crater. They run down the descent into the Whirlwind Maze where they discover the Sephiroth Clones fall from exhaustion, or be killed by Sephiroth. Upon reaching Sephiroth the party fights Jenova∙DEATH, after which Sephiroth is gone and they find the Black Materia on the ground. Cloud leaves the Black Materia with a remaining party member. Sephiroth shows Cloud and his party Nibelheim back before the incident, and shows Cloud he was never in Nibelheim five years ago, rather, it was Zack Fair.

Cloud is confident it is just an illusion, but Tifa, the only other party member to be in Nibelheim during the incident, does not refute Sephiroth's claims. Sephiroth tells Cloud he is just another drone like all the other mindless Sephiroth Clones. Cloud breaks down and Sephiroth tricks the party member with the Black Materia to give it up into the enemy hands. Rufus Shinra and his group of Shinra Executives land in the Whirlwind Maze with the airship Highwind.

Seeing the abundant Mako, Rufus thinks the Northern Cave to be the fabled Promised Land of Cetra legends. Cloud appears and pleads Professor Hojo to tell his number in the Jenova Project. Hojo laughs off how a specimen he considered a "failure" turned out to be the only successful Sephiroth Clone, but cannot recall much about Cloud.

Cloud hands the Black Materia to Sephiroth whose true form is residing within a cocoon of crystallized Mako. Sephiroth summons Meteor and the Planet summons its protectors, the Weapons, to defeat the threat creating a massive explosion of energy. Rufus and his entourage flee the chaos on the Highwind taking Tifa and Barret Wallace with them. Cloud is flushed into the Lifestream, and leaves the party temporarily.

Sephiroth seals the crater's entry with a forcefield and continues to remake his body to prepare for his ascension into godhood, his plan being to absorb the Spirit Energy that would well up to treat the wound created by his Meteor. Shinra uses the Sister Ray cannon to destroy the Diamond Weapon and blast through Sephiroth's forcefield. With the crater's defense down, Cloud and his party enter the crater to access the Northern Cave to defeat Sephiroth. Defeating Sephiroth releases Holy, an ultimate White Magic spell, and it bursts from the crater to destroy Meteor while the party escapes on the Highwind.

