In Crisis Core -Final Fantasy VII-, Zack first appears in a digital training session with Angeal Hewley, who seems disapproving of his reckless attitude towards his enemies and himself. Despite this, he approves of Zack as a member of SOLDIER, and requests to Director Lazard that he be promoted to SOLDIER 1st Class and be sent on his own mission in Wutai. Shinra had been at war with the Wutai for a good time by now, and SOLDIER 1st Class Sephiroth had already become a hero of Shinra for his actions there.
Though Zack was ecstatic over Angeal's suggestion, he received some interesting news during the briefing: 1st Class SOLDIER Genesis Rhapsodos had deserted Shinra, taking an untold number of 2nd and 3rd Class warriors with him. He had to be found and stopped.
After Zack took out the forces of Fort Tamblin singlehandedly, he met with warriors in strange armor. Sephiroth identifies them as copies of Genesis. Realizing that these were the soldiers that Angeal had last been seen fighting, and that he was nowhere to be seen, Sephiroth comes to the conclusion that Angeal left with his long-time friend, Genesis. Zack however, refuses to believe that his mentor would ever desert Shinra.
Zack now begins to fight against the forces of Genesis while meeting up with several other characters of Final Fantasy VII and uncovering the truth behind Project G. He first fights armies of Genesis Copies in Genesis and Angeal's hometown of Banora Village with the Turk Tseng one month after the Wutai mission. Zack's hopes are shattered, however, when he finds Angeal standing over the body of his dead mother, Gillian Hewley. Zack is horrified that Angeal could do something so horrible to his own family, and is badly shaken. He attempts to talk to Angeal, but the latter only says, "The mother could not continue to live...and neither can the son," and walks away. After Zack defeats Bahamut, whom Genesis had summoned, he questions Genesis about what happened to his dreams and honor. Unfortunately, Genesis only declares that they are monsters and flies away on a black wing hidden beneath his coat, leaving Zack as Tseng arrives to pick him up as the village is bombed.
In April 2002, Zack is at Shinra Headquarters when Lazard gives him the title of SOLDIER First Class (most likely to replace all the Firsts who are gone). Zack is not happy that he attained his dreams so early, and after so many losses. But then, Genesis's army attacks Midgar, and Zack has to fight them throughout the city. Along the way, he saves Cissnei, another member of the Turks. Sephiroth and Zack both head to the Sector 5 Reactor to find the rogue Dr. Hollander, who is suspected of working with Genesis. Zack chases Hollander through the Reactor until he runs into Angeal, now with a white angel wing and believing himself to be a monster. Refusing to fight his old friend and mentor, Zack lets Angeal drop down into the Slums.
Zack wants to repay Aerith with one date, but she tells him not to be silly, and then later accepts.Zack drops through the roof of a church, where Zack meets Aerith Gainsborough. Grateful to her for saving his life (although she insists that she did nothing but say, "Hello-o!"), Zack offers to pay Aerith back with one date. Zack suggests that Aerith should sell the flowers that only grow in the church. Later on, Zack gets his wallet stolen by a child, and would eventually find him, only to find that the child's wallet was eaten by a monster. In generosity, he lets the child keep his wallet in order to buy some medicine, or you can choose to take the wallet back from the monsters. That being done, it happens that the kid had a lot more money in his wallet than in Zack does in his. Zack then buys Aerith the ribbon that she is seen wearing throughout the series. It was also revealed in a DMW reel that Zack wants Aerith to wear all pink when he was around. However, their date is cut short when Zack has to return to the Midgar Plate to defeat Genesis. He protects Professor Hojo during this time. Angeal rejoins Zack, and together they drive Genesis out of Midgar. Zack has to face Bahamut Fury while Angeal deals with Genesis.