In Volume 1, she first appears briefly trying to comfort Shinji when he thinks that he’s "died". She then quickly transforms into a humanoid monster which repulses Shinji.
Kaji reveals to Shinji that Yui Ikari created Gendo as well as the Evangelion series.
When Evangelion 01 rejects Rei and the Dummy Plug, Gendo looks to the unit and addresses her as "Yui".
Shinji encounters a projection of Yui within Eva 01 which tries to convince him to stay. It destabilizes however, turning into the humanoid monster once again. Shinji sees another projection of Yui who tells him that he can stay if he wants, but he probably wants to be somewhere else. She promises to always watch over him.
In Fuyutsuki’s flashbacks, it is shown that she was a student of his prior to Second Impact. She appears as a gifted scientist and in a relationship with Gendo Rokubungi, who she finds endearing.
In further flashbacks, she tries to convince Fuyutsuki to work with Gendo but he refuses initially. After her death in the contact experiment with Eva 01, Gehirn was dissolved and reconstituted as NERV.
Ritsuko reveals that Rei was born in the place of Yui Ikari, and that Yui’s soul resides within Eva 01.