He is seen at HQ with the other echelons discussing Osamu's punishment. Shinoda believes that Osamu should only be pardoned, but he should also be promoted for preventing loss of life.
When Osamu and Jin are summoned to HQ following the discovery of Yūma, he is present. He listens to the information, and is shocked to find out that the Neighbor has the same surname as Yūgo Kuga. He explains that Yūgo was a senior to both Rindō and himself, and a colleague to Kido. Following this revelation, he believes that Yūma should be given leniency, but Kido still decides to retrieve the Black Trigger. In response, Shinoda orders Arashiyama Unit to support Jin as he battles HQ's top teams. After the battle ends in Jin's victory, he is at another meeting. He makes his position known; he is against capturing Yūma, and threatens to be Kido Faction's opponent if they try to go after Yūma again. Kido counters by threatening to use Amō. Shinoda is aghast because Amō has the potential to destroy the city. Jin comes in, however, and give Fūjin in order to ensure Yūma's safe enrollment into Border.
He is seen at orientation, welcoming the new trainees and wishing them luck as Border members. He is later seen at the meeting regarding the forecasted invasion, where he sees Replica's planetary diagram with wonder. After the meeting, he talks to Yūma, informing him of his gratitude to Yūgo and offering to boost Yūma to B-Rank. Yūma declines because he feels it is unfair, and Shinoda apologizes for not realizing that.
During the invasion, he stays in HQ and gives orders to units. However, when Enedra intrudes Border, he feels it is necessary to intervene and goes into battle. He rushes to the training room where Suwa Unit was engaging him. Shinoda enters and easily slashes all the dummies, scaring Enedra. He also has the AC turned on to blow Enedra's gas. Enedra heads to between Shinoda and the AC, allowing his gas to go upwind and enter Shinoda's trion body. He then has spikes come out of Shinoda. Shinoda reveals that he is simply a distraction; Kikuchihara and Utagawa slash Enedra's trion vitals, defeating him. Shinoda orders his subordinates to treat Enedra carefully as the latter is not in his trion body. However, Mira kills Enedra. Following this, Shinoda orders Kikuchihara and Utagawa to try and find as much information as possible from the corpse.
At the post-invasion media reception, he defends Osamu from journalists who believe that Osamu was responsible for the targetting of C-Rank agents.
He introduces the emergency meeting topic: another invasion. Two of Aftokrator's vassal nations, Rodochroun and Galopoula would be near Earth's orbit soon. During the invasion, he gives orders to the units inside and outside HQ, as well as listening to Amō's comments about the enemy.