Disaster strikes unexpectedly when NERV-02, NERV's second branch base in Nevada, mysteriously disappears in a flash, resulting in the loss of everything in a radius of eighty-nine kilometers and thousands of people. The incident coincided with an experiment to install an S² engine, capable of giving an Evangelion an unlimited power supply, into Evangelion Unit 04, one of the two new Evangelions which have recently finished construction in the United States. Panicking after the accident involving Unit 04, the United States government demands that Evangelion Unit 03, built in NERV-01, NERV's first branch base in Massachusetts, be removed from its soil as quickly as possible. As Unit 03 is about to arrive in Tokyo-3, Toji Suzuhara becomes the new pilot for it.