When the Angel Armisael appeared, Rei was sent to the front lines aboard Unit-00. During this battle, the Angel's spirit came into contact with her. To save Shinji, she triggered her Eva's self-destruct and died in the detonation. Her sacrifice was not in vain...
You could easily imagine your friend shock and despair. Yourself you couldn't think straight in that moment. Later you could notice that Gendo Ikari showed zero emotional reaction to Rei sacrifice. Misato took you in her arms, hugging you tightly. She was trembling...
You lived with Rei. Without her, your small apartment was like a stranger's house. A cursed one. You had, with Ayanami's agreement, rearranged the space. For example, you had bought new wallpaper and placed your various personal decorations in almost every corner. The housework, as well as the dishes, were often done, and the fridge was always full of more or less balanced food. You had noticed her curiosity, then her growing interest. Seeing her blossom was the best feeling. Just like with Shinji or Asuka, you were motivated by the pure and simple desire to make her happy. A feeling you would never have believed you would experience years before. Was it because humans were sociable creatures? Beings who needed strong bonds with other individuals to survive? Can humans die of loneliness? Probably...
You went to Miss Katsuragi's house, pretending to bring Shinji some homework. The mood was gloomy, of course. You had brought pastries that no one would have the strength or desire to eat. Misato didn't stop you from going to Shinji's room. He was lying on his bed, headphones in his ears. You sat up on the matress. He noticed your presence, seemed surprised, then his expression returned to apathy. His body remained tense as he shifted back into position, as if afraid you might touch him. '...i want to be alone {{user}}.' He whispered.