As the first production model Evangelion built specifically for combat against the Angels, Asuka is extremely proud of EVA-02. She's so attached to it that she refuses to take part in compatibility tests to see how well she synchronizes with EVA-00 and EVA-01, having no interest in piloting anything else. Asuka repeatedly refers to EVA-02 as hers and doesn't like the idea of anyone else sitting in her pilot seat. Is this because she wants to preserve her unique status over EVA-02 or is it because the soul of her deceased mother resides within it?

For the entirety of the series, Asuka remains ignorant to the fact that the soul of her mother resides within her Evangelion. Through the neural connection established through synchronization, she's been in contact with her mother every time she sits inside the entry plug. It isn't until she begins to suffer from a deep depression that Asuka's synchronization scores drop to the point that she is no longer able to make EVA-02 respond to her commands at all. How do we explain this, in terms of the connection between pilot and Eva? In an interview, Yoshiyuki Sadamoto has made the following statement:

"On the floor of the midbrain is the ventral tegmental system, that neurobiologists call region A10. Cells soaked in dopamine, certain emotions are processed here; such as the thoughts of two lovers--or of a parent and child. And it is the synchronization of the threads and bundles of A10 that splice pilot and Eva together; to become one entity, to fight. In other words, the power of love drives this weapon of mass destruction. Well, what a simple and corny and emotional and wonderful story."

This would mean that depression would prevent Asuka from feeling the emotions she needs to feel in order to achieve synchronization. Asuka's identity, pride and self-esteem all rest on her ability to pilot the Evangelion. When she begins to lose her ability to pilot, so too does she begin to lose the identity that she has created for herself. While Asuka was far from having achieved inner happiness when she had high synchronization rates, her emotions still allowed her to connect to EVA-02 on a parent-child level. When her depression began to grow, guilt and despair eclipsed all other emotions to the point where she seemingly tried to kill herself.

In End of Evangelion, when Asuka is put into EVA-02 for her own safety, she is curled up into a ball. Up to this point, she's has been in a catatonic state and it isn't until she's back in the pilot seat that she realises she's still alive and doesn't want to die. In response to hearing her daughter's pleas to live, Kyoko's spirit responds to Asuka and tells her that she won't let her die (although we do briefly hear the insane part of her soul asking Asuka to die with her). It is at this moment that Asuka realises that her mother has been with her inside the Evangelion, watching over her and protecting her from the moment she began to pilot it.

Asuka is ecstatic when she makes this revelation, breaking free from her depression. She's once again able to achieve high synchronization rates with EVA-02 and proceeds to defend herself against the UN armed forces (and subsequently the nine mass production Evangelions) attacking NERV. This is where her mother has been all along!