Matsunaga first appeared to recruit Kazuki Komon, as well as being present for his forced exame. He personally congratulated him on passing the test and gave him his Pulse Brieger.
He mainly spoke with Captain Wakura about Komon's progress and to Illustrator about the precession of events concerning the Beasts, Ultraman and the Dark Giants.
Matsunaga also had a desire to understand the secrets of Ultraman's light and perhaps the source of the conflict between Ultraman, humanity and their shared enemies the Space Beasts. To this end he dug up information about the Shinjuku incident and the giant codenamed: Next. He also kidnapped Himeya Jun, the then Deunamist of Ultraman Nexus to analyse the 'Light of Ultraman' when he was left weak from his continous battling and growing injuries. At first his science team attempted to scan his memories, but Jun's trauma made that worthless. Matsunaga called upon the Beast Signal Emitter to force a reaction despite warning that such a thing would be fatal for a normal human.
When Jun flatlined Matsunaga panicked and tried to revive him and used Illustrator's advice about the Signal Emitter, this time using the energy wave Jun used to transform. Jun was saved but Nexus whisked him away in a bright light. However Matsunaga gained the information about Ultraman's destructive beam but he did not gain the secrets he actually desired.
Later, after the battle between Nexus and Dark Mephisto, Matsunaga was there for the interrogation/debriefing of Nagi, Komon and Wakura, who all talked about Ultraman. Matsunaga gained his greatest insight about Ultraman from Komon, who relayed Jun's last words. However, Illustrator soon informed him that a spy had destroyed all their information they gained from experimenting on Himeya Jun.