Thanks to their monopoly on mako energy and a strong military force, the Shinra Electric Power Company is quickly exerting their influence around the world. Construction is also rapidly advancing on their base, and symbol of prosperity, the mako city of Midgar, which will soon become Shinra's seat of power.
The Shinra Company possesses an organization of soldiers with powerful combat ability known as SOLDIER, and amongst them, the especially excellent SOLDIERs are known as SOLDIER: First Class, inspiring respect and envy from the masses. One of the young people yearning to be First Class is Zack. He works hard at his daily duties with his senior, Angeal, a First Class and an excellent leader.
At that time, the SOLDIER Mass Disappearance Incident occurred when, during combat operations in Wutai, Genesis, a first class member of SOLDIER, went missing without a trace along with many other SOLDIERs. The Shinra Company's top management assessed the situation and decided to send out SOLDIER in order to bring an end to the war and clarify the scandal, and so, Angeal and Zack, as well as Sephiroth, whose name would come to be known throughout the world as a hero, were dispatched to Wutai.
During the duration of the game, events similar to Last Order: Final Fantasy VII take place, as well as Zack meeting Aerith, becoming best friends with Cloud, Zack discovering the truth about both Angeal and Genesis' orgins, The truth behind the mysterious "Project 'G'", Sephiroth's hatred of the Shinra company beginning, and many other events. There are also scenes in Crisis Core of Zack that Cloud had as flashbacks in Final Fantasy VII Advent Children and Final Fantasy VII.
At the end of the game, Cloud and Zack reach the Wastelands near Midgar, after escaping Shinra. However, Zack is shot by the pursuing Turks and Shinra soldiers while Cloud is left unharmed because of his vegetative state. Aerith is seen waiting at her church, praying for Zack.
After some time Cloud snaps out of his rigid state and heads towards Zack. When Cloud reaches Zack, Zack (while giving Cloud his Buster Sword) tells Cloud to take all his pride and dreams for him and continue living, and then finally dies. Cloud literally cries out in anguish. After his brief mourning, Cloud says his thanks to Zack and tells him to rest. Zack talks aside that he is finally a hero, while the scene goes to Cloud who is carrying the Buster Sword and making his way towards Midgar.
After the credits roll, the intro to Final Fantasy VII plays. Aerith is seen exiting a building into the streets of Midgar, while Cloud (who is not too far from her) rides on top of a train stating, "I am Cloud. SOLDIER. First Class." marking the beginning of the original game, Final Fantasy VII. The game ends with the words, "To be continued in Final Fantasy VII..."