In the anime, after Shinji leaves NERV, Gendo transfers Rei to EVA Unit 01, with the dummy plug as the backup system. However, EVA Unit 01 rejects these two outright, refusing the connection altogether. But when Zeruel attacks Dogma HQ, EVA Unit 01 comes back online and engages the Angel, with Shinji as its pilot.
My question is this, why did EVA Unit 01 reject the other two's connection but allow Shinji to connect on the first try?
EVA Unit 01 contains the soul of Yui Ikari, who disappeared during a contact experiment: in ep. 20, after Shinji achieves a high synchronisation rate and is absorbed into LCL in the EVA Unit, he comes into contact with his mother, and Gendo also makes a statement during one of these refusals that indicates a connection with Yui. Thus Unit 01's refusal to work with anyone or anything other than Shinji is linked to Yui's mother-child relationship with Shinji (a relationship she has with neither Rei nor an empty dummy plug) and Yui's own preferences.
