The people who had gone missing in Tokyo-3 did not return after Alien Yapool vanished. Some of their DNA was found in the rain of blood.
As for the others... they had disappeared without a trace. NERV found only scraps of evidence in the Super Beasts' remains, with no further leads beyond that.
The incident caused widespread panic in Japan, and a flood of inquiries and accusations poured into NERV.
NERV had no choice but to reveal Alien Yapool's existence, while assuring the public that the Ultra Warriors had utterly defeated him.
Some of the panic subsided, but the criticism only grew worse. Neither NERV nor the UN Army had noticed this enemy from another dimension at all, and even after reports of missing people came in, they had failed to take decisive action.
That only intensified the criticism.
Left with no alternative, NERV used the media to heavily publicize the victories achieved by Pedanium Unit-03.
Without any help from an Ultraman, Pedanium Unit-03 had killed the Missile Super Beast Verokron and the Moth Super Beast Doragory.
This did restore NERV's reputation somewhat, but only somewhat.
Gendo Ikari and Fuyutsuki did not particularly care. Once the Angels were eliminated, NERV was certain to be reorganized, if not disbanded entirely.
Before that happened, however, SEELE would undoubtedly cause plenty of trouble. The only saving grace was that the national leaders secretly informed of the Human Instrumentality Project remained firmly opposed to it. They had chosen to side with NERV, which had already betrayed SEELE in secret.
Their one remaining worry was Hayato Noda. Yet NERV had exhausted every means available and still found no clues about him.
He was the greatest source of uncertainty.
In Shinji's class, the damage inflicted on the city by the ongoing battles had left them