Detective Conan: Black Iron Submarine

The Black Organization kidnapped Haibara because the All-Age Recognition system could identify her face as resembling Shiho Miyano, her original identity. By capturing her, the Organization could exploit this identification to further their goals, either by using her as leverage or confirming her true identity.

Earlier in the film, Naomi's flash drive revealed that the All-Age Recognition system could link Haibara to Shiho Miyano.

Pinga is Grace, one of the engineers working on the Pacific Buoy project. She was secretly a Black Organization operative who controlled the operation from behind the scenes, created the backdoor access that tampered with surveillance, and murdered Leonhardt before attempting to escape during the climax.

Grace authored the confession letter claiming responsibility for the backdoor, which initially seemed like Leonhardt's confession.

Vermouth disguised herself as Shiho Miyano and appeared in security footage to create a flaw in the system, discrediting the idea that Haibara is Shiho Miyano. However, her true motive for helping stage this flaw remains unknown and is left for Conan to discover on his own.

Vermouth had earlier informed Gin that the system could identify similar faces but not the exact person, setting up this deception.

Grace, who was Pinga, created a backdoor access in the Pacific Buoy system that allowed the Black Organization to tamper with the surveillance footage. When Conan tried to trace the kidnappers, the security cameras showed no submarine or vehicles because the footage had been manipulated.

Leonhardt was initially suspected of creating the backdoor, but a confession letter later revealed Grace as the true author.

After Vermouth informed Gin that the All-Age Recognition system could identify similar faces but not the exact person, Gin decided the project was too risky and ordered a submarine attack to destroy the Buoy, eliminating both the threat of the surveillance network and anyone who knew about its capabilities.

Vermouth's revelation about the system's limitation directly preceded Gin's decision to attack.

After the rocket hit the submarine and Pinga died in the explosion, Conan was knocked unconscious underwater. Haibara, who had been kidnapped earlier, performed a dangerous ascent and rescued Conan, bringing him to the surface and saving his life.

Haibara was taken to the submarine, placing her in position to rescue Conan during the attack.

All-Age Recognition is a facial recognition and AI reconstruction system developed at Pacific Buoy that can identify people even when their appearance has aged or altered. The Black Organization was particularly interested in it because it could potentially identify Haibara as Shiho Miyano, her original identity before becoming Ai Haibara.

The system was introduced during the launch briefing as the project's most controversial and powerful feature.

Naomi Argento's father was targeted because the Black Organization wanted to eliminate anyone connected to the Pacific Buoy project and its sensitive technology. He survived the assassination attempt, and the project was later moved to another country for safety.

The attack on Naomi's father occurred in the post-credits scene as part of the Organization's cleanup operation.

Bourbon and Vermouth kidnapped Naomi Argento to use her as leverage and push the Pacific Buoy project forward under Black Organization control. They held her captive in a submarine as part of a larger plan to steal crucial data from her USB drive necklace and manipulate the surveillance system.

Naomi's flash drive contained critical information about the All-Age Recognition system that the Organization needed.

Leonhardt was murdered because Grace (Pinga) needed to eliminate him and cover her own tracks as the Black Organization's operative. She drugged him and made his death appear as suicide or natural causes, while also framing him with a fake confession letter about creating the system's backdoor.

The confession letter found near his body initially led investigators to believe Leonhardt was responsible for the security breach.

Naomi learned that Haibara is Shiho Miyano because they had studied together in the United States. When Haibara stood up for Naomi during their time as students, Naomi recognized her true identity and understood why the All-Age Recognition system could identify the resemblance between Haibara and Shiho.

This connection is revealed in the post-credits scene when Naomi reflects on their shared past.

Conan investigated Pacific Buoy after receiving information from Subaru Okiya that the Europol agent's murder was connected to a Black Organization operative called Pinga. When he discovered Inspector Shiratori and Chief Kuroda were secretly visiting the facility, Conan realized the case touched a global network and decided to track the conspiracy firsthand.

The warning from Subaru Okiya about Pinga and the wider conspiracy prompted Conan to dig deeper into the Interpol facility.