He is shown to run away from not only difficult situations, but also from developing relationships and his own emotions.
He tells himself, "I've got to go back", but instead attends a late-night showing of a movie about Second Impact. Shinji boards a local train and rides it all day, repeatedly listening to tracks 25 & 26 on his SDAT, leaving only when the train is taken out of service. They ask her about Shinji, and she lied and told them that he is at the training facility. Being worried about his sudden absence, Toji and Kensuke go to his place, but got surprised for seeing Misato for the first time. She then goes to check on his room only to see it empty with Shinji's ID card and a letter to her. Misato wakes up on a rainy day, and wonders if Shinji is going to skip school again after five days of his battle against Shamshel.
However, at the last minute, Shinji does not board his train to leave Tokyo-3 and decides to stay. Shinji is soon recaptured by NERV, but he quits being a pilot. Overstressed from being made an Evangelion pilot, from the events of the previous episode, and arguing with Misato, Shinji runs away from home.