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.

Hajime annoys Sugane when she allows the MESS to escape. Later, she teaches Sugane about a popular social app called GALAX, which allows users in the vicinity to help each other, and decides to take him to an offline meet-up.

Hajime befriends the MESS, which she nicknames Messy, and the abduction cases involving the MESS stop. The other Gatchaman begin to wonder whether they were hostile at all. The next day, GALAX users at Hajime and Sugane's school receive word that some spoiled milk has been sent to their school, and they act together to warn the other students.

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.

Utsu-tsu risks her life to heal the wounded, and Hajime's identity is revealed to the world. Rui helps Hajime and Utsu-tsu evade the press, but then demands they give up being Gatchaman, because GALAX makes Gatchaman unnecessary.

Rui decides to stand against Katze using the might of Crowds, but Katze uses the power of Gatchaman to overwhelm them. The Gatchaman team rushes to Rui's rescue, but find themselves outmatched.

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..

After taunting Hajime on GALAX, Katze sets the Neo-Hundred after the Prime Minister. The Gatchaman team are forced to protect him while trying to find a way to stop the Crowds without harming the users.

Rui regains control of X, and uses the GALAX network to help the Gatchaman team in the crisis. Hajime convinces the Prime Minister to broadcast a message on the Gatchannel, asking everyone to join the GALAX network and band together. But Katze takes the form of the Prime Minister, once again urging people to use Crowds.

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.

Partially a recap of season 1 episode 12, this special depicts the confrontation between Hajime and Katze, and explains Hajime's mysterious behaviour at the end of episode 12.

After a brief summary of the events of the first season narrated by Sugane, Prime Minister Sugiyama's plane is attacked by two fighter jets hijacked by the mysterious VAPE organization, composed of anonymous users of red-colored Crowds. Upon being informed of the situation by X, Rui transforms himself into a Gatchaman and transports himself and Hajime to inside the plane in order to fend off the attackers.

Misudachi Tsubasa is an ordinary high school student in Nagaoka City. But everything changes when an alien spaceship lands crashes down right next to her house and the Tachikawa Gatchaman crew come to investigate...

Tsubasa has been abruptly thrust into the Gatchaman role, but her positive mindset moves her to embrace her new life and vow to act as a hero. Meanwhile, Rui continues his investigation of the mysterious organization VAPE, but he is suddenly accosted by the red CROWDS...

Tsubasa arrives in Tokyo with Gelsadra, where they are promptly enlisted to appear as guests in the popular Millione Show. There, they make a favorable impression, and they're soon familiarization themselves with their new teammates in the Gatchaman HQ, Tachikawa CAGE. However, Suzuki Rizumu, the VAPE leader, is about to make his move...

Believing in her brand of justice, Tsubasa races to save a fading life with a strong wind at her back. Her rescue of Rui with Gelsadra is broadcast live nationwide, inspiring admiration for the new heroes among the people of Japan. As she strikes a blow to end the conflict, a new chapter begins...

The prime minister elections have finally begun. While Sugayama's predicted to win by a landslide, Gelsadra uses his powers to discern what the people want. What he promises his supporters is enough to create a rift even among the Gatchamen.

With the support of a majority of voters in the smartphone election, Gelsadra becomes the prime minister. He quickly absorbs knowledge and gains an understanding of politics in Japan.

Japan undergoes rapid change as Gelsadra continues his reforms based on his slogan, "Our Hearts as One, Create Our World, Together." With his popularity on a meteoric rise, his constituents are full of smiles. Tsubasa firmly believes that their shared dream will soon come true, but some cannot help but feel a sense of disquiet over the rapidity of change...

Due to what happened to Gelsadra, the red speech bubbles suddenly produced mysterious life forms, which start appearing all over Japan and start interacting with everyone. The G members move out to deal with the mysterious beings, but things take a rather unexpected turn...

The general public has come to accept the Kuu-samas into society, and they seem to be helping with Gelsadra's wishes to help everyone become one. However, in order to make everyone become one, the Kuu-samas take the next step. The Gatchaman try to warn the public about the Kuu-samas and their actions, but they find out now that this has been set into motion, it's not easily stopped. The Gatchaman now consider Gelsadra and the Kuu-samas dangerous, which ends up making them unfavorable to the general public that loves both Gelsadra and the Kuu-samas...

Rizumu's ideal world slowly starts coming to fruition. The small opportunity presents itself, and is magnified, causing chaos to spread quickly. However, Gelsadra, who is in the middle of all of this, believes he is just doing what the people want and smiles, despite some terrible things that have occurred. Meanwhile, Tsubasa who had separated herself from the Gatchaman and Gelsadra goes back home to Nagaoka to face Yuru-jii and herself...

A massive throng of Kuu-samas assemble from all across the country and swarm the town, and the Gatchamans go all-out to take them out.

Having accepted the masses' wishes, the Gatchamen head to battle with a strong resolve to put everything they have on the line in order to grant them.