Arc 3Angels and Broken Bonds
Huang Zhetian and Asuka returned from China to face the Night Angel, whose attack left Shinji and Huang trapped and brought their relationship to an end. After Unit-03 became an Angel and Toji was caught in the battle, Huang was badly injured, Shinji quit piloting, and the Power Angel attacked while Shinji struggled with his decision to leave his teammates.
- Huang Zhetian took Asuka to China, where they found his former home empty, learned more about their losses, and promised to build a future together.
- Huang Zhetian and Asuka returned to Japan, where Shinji received a simulation of Yui, Asuka broke up with Huang, and Misato and Kaji reconciled.
- Night Angel trapped Shinji and Huang in its inner space, where Shinji faced painful memories and Huang confronted his other self before Unit-01 destroyed the Angel.
- NERV discovered that Unit-04 and its branch had vanished, while Kaji uncovered the truth about the Marduk Institute and Misato learned that Toji had been chosen to pilot Unit-03.
- Unit-03 became the Angel Shamshiel, disabled Asuka and Rei, and forced Gendo to use the Dummy System, which made Unit-01 attack Huang and the other living pilots.
- Shinji quit piloting after learning that Gendo had used the Dummy System against Toji, while Huang suffered severe injuries and gave Kaji a letter to destroy.
- The Power Angel attacked New Tokyo-3, severed the heads of the Special Unit and Unit-02, and left Shinji at the shelter regretting that he had abandoned his teammates as Kaji began telling him about his past.