McGarrett woke in the middle of the night to the sound of a burglary. The thieves took the tool box containing the evidence of McGarrett's mother's murder after knocking McGarrett unconscious. Talking to the rest of the Five-O McGarrett said he only told the members of the team about the tool box, but he quickly realized he had also told his sister about it.
Racing to his sister's house McGarrett and Danno discovered evidence of a struggle, but there was no sign of Mary. She had been kidnapped, but had the foresight to call her brother while locked in the kidnapper's trunk. McGarrett and Danno chased down the kidnappers in a helicopter and rescued Mary.
The tool box was still missing, but Mary had taken photos of each of the pieces of evidence which left McGarrett clues he could still follow.
An examination of the tattoos on the bodies of Mary's kidnappers led the Five-O to a club where lower level Yakuza members met. There they were able to identify a third kidnapper who had lost a tooth in the struggle to kidnap Mary. The last number dialed on his phone was made to Hiro Noshimuri a prominent business man, whose name also appeared on a cipher from a postcard in the tool box basically naming him as the head of the Yakuza in Hawaii. McGarrett raced to confront Hiro Noshimuri, and discovered he was friends with the governor.
McGarrett explained his actions to the governor, and she trusted his instincts but cautioned him against making any rash moves. She was not sure she could protect McGarrett and the Five-O if he did otherwise because of the powerful connections Hiro Noshimuri had in the state.
While talking to a friend of the family who had witnessed a H.P.D. officer fiddle with the underside of McGarrett's mother's car Yakuza appeared and shot at McGarrett and Danno. One of the men was killed, and McGarrett intercepted a call from the men's boss. Meanwhile, Kono discovered the tool box. It was empty, but had Hiro Noshimuri's finger prints all over it which was enough for McGarrett to arrest him.
McGarrett put his sister on a plane for Los Angeles in order to protect her from further involvement, and the officer that had been ID'ed as the man who planted the bomb on McGarrett's mother's car was killed in a car accident.