Ran wakes up in a hut in the woods and discovers someone has treated the wounds from when she fell. Eventually, Kazuha finds Ran and calls Kogoro in. Heiji radios them from the next room. They all go over and find that the room is filled with pictures of Shinichi with knife marks in them. Heiji figures out the case, and they head back to Hinohara's house.
Heiji figures out out that the Shinichi with the group is not the real Shinichi, but the supposedly missing Makoto. Makoto had undergone plastic surgery to look like Shinichi and faked the amnesia in order to frame Shinichi in revenge for his previous deduction that the deaths of his adoptive parents was actually a murder-suicide instead of a burglary. He attacked the reporter because she knew the truth about who he really was and would have outed him. The Shirigami that Ran encountered in the woods enters the room during Heiji's explanation and reveals that he is the real Shinichi, and had been hiding out in the woods disguised as the Shirigami while keeping an eye on everyone to prevent Makoto from reacting violently if he were to appear and ruin his plans.
The crime one year previously that Shinichi had solved and was hated for was explained in full: he wasn't wrong in his deduction, but he did lie about the motive. The mayor did kill his wife and himself, not because he was terminally ill like Shinichi had told everyone, but because he discovered that the child he believed to be his son was actually the result of an affair his wife had. Makoto was told this, but he was in such a state of shock at the time that it didn't register.
After Makoto is arrested, Ran, Heiji, Shinichi, Kazuha, and Kogoro walk back toward the hotel. Before they can reach it, APTX 4869 starts to wear off, and Heiji helps Shinichi escape to the bathroom to change back. Haibara had been hiding there, and she gave Shinichi another antidote. Then, she says to return to Tokyo before he changes back if he wishes to keep his identity a secret. The group are all heading home in Kogoro's rental car, when they discover a man who was strangled within his car on the highway. They stop to investigate.
