In reality, it was Naomi who was struck by lightning and declared brain dead all along, while Ruri was the one attempting to save him. Essentially, everything depicted in the movie was essentially a dream within a dream.
While both the OVA and the entire movie were animated in 3D, the scene before the credits shifted to 2D animation. This suggests that the simulation exists in 3D animation, while reality is represented in 2D. Hence, any scenes presented in 3D form aren't real – why else would they switch to 2D animation at the end? It wouldn't make sense otherwise.
Throughout the movie, Ruri was the same crow observing Naomi for three months. It was implied that whoever delves into the past can alter their avatar as they see fit.
Ruri ventured into the past to gather data and synchronize Naomi's memories in an attempt to rouse him from his comatose state. Additionally, she was the one who guided him using the crow avatar from the movie's beginning to its end.
Please note that this is simply my interpretation and shouldn't be taken as definitive.
