While Ayesha may have begun her journey as a simple herbalist, the influence of people like Wilbell and Keith causes her to gradually awaken as an alchemist. She goes to the "Zweiteturm" in search of further knowledge.
Thanks to her adventures and the knowledge she gains at the Zweiteturm, Ayesha begins to realize that the mysterious "flowers" may be related to Nio's disappearance.
Ayesha finds more flowers, and even manages to talk to Nio, but the time they're able to spend together becomes shorter and shorter, and the sense of impending danger grows apparent.
Ayesha continues to gain more experience on her adventure, growing further as an alchemist. She meets many people, and grows as a person through interaction with them as well.
As Ayesha grows as an alchemist, Keithgriff offers advice to save Nio. However, he also explains that this is the same alchemy that brought the world to ruin previously, and the thing that had kidnapped Nio was one of the "evils" of alchemy left from the past era. Ayesha grows doubtful, and is unable to make a decision.
Will alchemy really bring the world to ruin? Is there any way to save Nio?
*Some screens may be artistic impressions, or from the original "Atelier Ayesha."