"I have twenty-three tiny wishes, but you probably won't remember them all, so I put them all together into one...I'd like to spend more time with you." —Aerith's Note to Zack
In 0000, a fifteen-year-old Aerith first meets Zack Fair when he falls into her church from the Sector 5 Reactor. When he awakens, Zack at first mistakes being in heaven and Aerith as an angel, but Aerith quickly corrects him. As a repayment for saving him, Zack suggests a date, but Aerith brushes him off. All the same, she shows him around, and Zack buys Aerith her trademark pink hair ribbon. The two go to the park and Aerith tells Zack she is afraid of SOLDIER members, as they frighten her for being experiments who love to fight. Zack says he is from SOLDIER, and she apologizes.
To break the awkward silence, Aerith says his eyes are beautiful. Zack lets her have a closer look, and as they draw nearer, Aerith becomes aware of their close proximity and pushes him for teasing her. Zack comments that his Mako eyes are like the sky. Aerith smiles and says they are "not scary at all". After this, Tseng calls Zack back to the Shinra Headquarters, but he promises Aerith she will see him again.
Aerith and Zack continue to speak frequently over his cellphone and see each other for the next two years, and after Angeal's death, Zack returns to the church and Aerith holds him as he cries. Zack suggests to Aerith that she sell flowers to make money, as flowers are rarely seen in Midgar and are a luxury item. Aerith is reluctant to sell flowers above the plate, as the open sky frightens her. Zack eventually constructs flower carts for her to sell from, and the two head out to the slums to sell flowers, although it does not go well.
Aerith asks Zack for "a few tiny wishes", and Zack has her write them down for him on a piece of paper. This is the last time the two would see each other, as later that day Zack is dispatched to Nibelheim with Sephiroth. In the years after Aerith eventually overcomes her fears and begins venturing above the plate to sell flowers.
Aerith first appears in Before Crisis in Episode 6, selling flowers to Rude when he goes on his date with Chelsea, although she is not called by name. In Episode 11, on August 9th, 0002, the player Turk meets Aerith coming out of her house, surprised by the blooming flowers. Aerith tells the Turk she wishes to leave Midgar to see the world, as she can hear the wind calling to her. AVALANCHE arrives searching for her, and the player Turk helps Aerith evade them.
Eventually Shears defeats the player Turk and Aerith is taken to her church to meet the leader of AVALANCHE, Elfé. Elfé tells Aerith AVALANCHE wants to bring down Shinra and protect the Promised Land, and thus it is in her best interests to ally with them. Aerith notices an "old voice" coming from Elfé, and this inadvertently leads to the discovery of the Turk spying on them from the rafters. After the Turk battles Shears and Fuhito, Elfé is stricken by a sudden weakness, and AVALANCHE retreats. Tseng arrives and the Turk allows Aerith to flee while they distract him. Aerith in Crisis Core's ending.
When Zack escapes Shinra custody years later, the final Angeal Copy who was left watching over Aerith when Zack left Midgar leaves behind a letter from Aerith as it fades. As Zack reads it he finds out Aerith has been doing well selling flowers in Midgar, and during the four years of his disappearance she has written Zack eighty-nine letters, though he never receives the rest of them. Tseng is in possession of the letters and sends the Turks to find Zack before the Shinra army so they can save him and deliver them, but the Turks ultimately fail.
In the game's ending Aerith is seen tending the flowers, then turning and looking towards the sky and clasping her hands. It is at this time, outside Midgar, that Zack is gunned down by Shinra forces. Although, in Final Fantasy VII, Aerith states she is unaware of Zack's fate, it has been speculated that the last scenes in Crisis Core -Final Fantasy VII- have retconned this to her sensing his demise.