EVANGELION: 3.0 (-46h) is an original video animation (OVA) included as a bonus feature with the DVD and Blu-ray release of Evangelion: 3.0+1.0 Thrice Upon A Time on 08 March 2023, the two-year anniversary of the film's initial theatrical release. It was announced on 04 October 2022 and included on a separate disc together with a video re-release of the anime short EVANGELION: 3.0 (-120 min.)

On the day Touma Kamijou and Index see Academy City's space elevator, Endymion in the distance, they meet a Level 0 girl with an amazing singing voice, Arisa Meigo. As the three enjoy their time together after school, magic-user Stiyl Magnus suddenly attacks them. His target: Arisa. Why would a girl from the science side be targeted by someone from the magic side, Touma wonders. In the chaos of Stiyl's attack, he tells Touma, Index and Arisa that she might cause a war between the magic side and the science side.