The next case involving Eisuke begins with no one being able to get a hold of him since the beginning of winter break. Before winter break, Ran said that he told her he found a clue a the Beika Center Hospital ( where Rena is). He said that he found one of his father's colleagues. Eisuke told Ran that someone at the hospital was using the same e-mail address as the boss of his father. And Eisuke knows the address because he could hear the key pad's tone when his father would send a message to it and it sounded like the child's song "Nanatsu No Ko (Seven Children)" So, Conan knows that someone connected to the black orginization is there. Eisuke went to the hospital and showed a nurse the photo of his sister in order to find Rena, but seemingly got no information and left. But he was actually still hiding in wait there.
As Conan an the FBI investigate to try to find out which patient is actually a member of the black orginization, Mizunashi Rena regains consciousness. But she continues to feign unconsciousness. Conan is able to notice that and uses it to draw out the truth later.
Conan learns Eisuke had leukemia and was at a hospital in Tokyo with his mother for a surgery. That's when Conan realizes that Rena is his real sister and that his blood type must have been changed to AB. He got a bone marrow transplant from his sister. HLA, or the Human Leukocyte Antigen, is often easily a match with siblings. Upon treatment, Eisuke who's O type blood was being destroyed from the radiation was changed to AB type in order to receive the transplant from his sister. Also that's related to the scar Conan noticed on Eisuke's chest in the earlier case.
It seems that Akai Shuichi had a girlfriend who, a few months ago, in order to be kept quiet, was killed by the black orginization. And so, Shuichi seems to have a personal grudge against them. That girl herself wasn't to deeply involved with the orginization but Shuichi was getting close to her to find out about her younger sister who was a scientist deeply involved with the orginization. During a period of three years, from 5 years ago to 2 years ago, Shuichi was under the false name of Moroboshi Dai. He was given the code name Rye by the black orginization. He had well infiltrated them and was on an assignment with Gin. They hoped that if he could full even Gin that he would be able to make it all the way to their boss. Shuichi went to the meeting place and the FBI secretly stood by, but the black orginization never showed up. They seemed to realize that Shuichi was with the FBI. However, his girlfriend wasn't killed at that time because her sister was so important. The girl was given a job and if she completed it she was told that her and her sister could leave the orginization but if she failed they would be killed. Her job was a billion yen robbery. That girl was of course, Miyano Akemi, and the younger sister, Haibara.
The day before she went on that job that led her even to Detective Mouri's Office and to later be killed by the Black orginization, she sent a final message to Shuichi. It said "It seems I'll be able to leave the orginization so maybe I could really be your girlfriend. Akemi"
Eisuke enters the room and starts to attack Rena. It is at that point that a lot of information is uncovered and Conan and Shuichi devise their plan.
"The Company" Eisuke's father was part of is the C.I.A. Hondo Eisuke's father, who's name was Ethan Hondo, was a second generation Japanese-American who 30 years ago joined the C.I.A. Three years later he got married and seemed to be hiding out in Japan. That was to infiltrate and collect data on the Black Orginization. That's why he had the email address of the orginization's boss that Eisuke overheard the dial tone of. However, 4 years ago at an unused warehouse in Yokohama he was scouting out the area for the black orginization's next transaction (he was still posing as one of them). At that time Rena (who is also a CIA agent) was temporarily posing as a member of the black orginization but only to set up her father with a new partner, but she was bugged without realizing it and in order to protect her he killed himself and made it look like she killed him for betraying the orginization. So, from that point on she continued to pose Mizunashi Rena, the TV announcer and Kir the member of the black orginization.
As for why Conan knew she was a CIA agent beforehand.
Conan knew that she is someone who can tell if someone is lying based on breathing, heart rate and pupil dilation, because when she said thank you to him for saving her when she was interviewing the man targeted for assassination by the black orginization in the park, she had obviously seen through Conan's false identity and that sort of technique is common for CIA agents. Also the phrase she muttered around the black orginization "Our achievements never she the light of day, but our mistakes are quickly well-known", which is a common motto for the CIA. Also, when Vermouth knocked on her bike and asked if Kir was one of those, she was saying "are you a NOC", or CIA agent.
So, they agree that she will go back to posing as a member of the black orginization, and ans help the FBI as a CIA agent in their investigation. But they can't just had her back over to the orginization openly so they come up with a plan to make it seem like she escapes while the FBI is trying to transport her to an other hospital. (They were transporting her because the secret black orginization mole in the hospital had been caught and the orginization made some moves in order to locate Rena and were beginning to move in to take her away anyway, so Conan and Shuichi use that to their advantage)
Their plan works and Rena, whose real name is Hidemi, is back with the black orginization, who thinks she is one of them.
Eisuke knows that his sister and father were CIA agents and that they were after some orginization but that's all he knows. And, for now, his is being protected by the FBI. Also, that is who Rena asked Mouri to keep an eye on a while back.
