Hajime Ichinose is a rather eccentric schoolgirl who is obsessed with notebooks. One day, she is approached by a mysterious man named J.J. who pulls out a journal called a NOTE from her body, declaring her to be the new member of the elusive Gatchaman team.

The mysterious "Crowds" are revealed to be strange beings controlled by the GALAX users. Meanwhile, Joe fights against the strange alien known as Berg Katze, but is beaten back when Katze uses a NOTE of their own.

While Hajime clashes with Sugane and Paiman about why the Gatchaman are so secretive, Rui is faced with a dissenter in one of the "Hundred", who believes that Crowds should be used to kill evil politicians.

Katze takes on Rui's form to steal control of GALAX and form a new "Hundred". Hajime suggests the best way to fight is for the Gatchaman team and Rui to reveal themselves and go public. Rui learns a troubling fact about the side effects of Crowds.

Katze continues to distort Rui's vision, giving Crowds to people Rui had decided were too dangerous to have it, and staging attacks on government targets. Hajime sets up a 'Gatchannel' live stream, where Rui publicly apologies over the usage of Crowds and urges those that have it to not use it, and Hajime explains that the Gatchaman will confront Katze even if she is still unsure they can win. Hajime's determination inspires Sugane to confront J.J..

As more citizens use Crowds and fight against each other, chaos breaks out. O.D. risks everything to retrieve Rui's NOTE from Katze. Hajime sends her mother a cryptic message, then leaves for a final showdown with Katze.