One dead, Kouhei Kamata, and according to Heiji, the killer is among his two friends, and an ex-girlfriend, Ayako Ninagawa, who served the drinks. Apparently, the man was killed by poison that was put in his drink. It's suggested that it could have been the cream or sweetener he put in his drink, but the packages of cream and sweetener are then found in his pocket. It turns out that he was mistakenly given cola instead. It couldn't have been the cola, because two cups were labeled "Ice Coffee", and so he could have received either one.
Kogoro proposes that he might have committed suicide, and so they go to his car to search for anything suspicious. During this interlude, The Black Knight looks out the window at the officers running in the rain to the car. And Conan watches The Black Knight. Heiji walks over to Conan, and starts to discuss the case, looking for input. Conan, though, is not interested, and brushes a puzzled Heiji away. Kazuha comments about Heiji and Conan's closeness, to which Ran only smiles.
The officials return, having found a vial of poison in the dead man's car, and are about to declare it a suicide when a familiar voice asks them to wait. The all look up and see the Black Knight walking towards them. He explains that this is actually a murder, set up to look like a suicide, and there is a murderer in this room. And as he gets close, he stops, and removes his mask. It's Shinichi Kudo.
Everyone gasps. Ran thinks "No! This can't be! Shinichi is..." and looks over her shoulder at Conan. Shinichi apologizes to Inspector Megure for being gone so long, and then approaches Ran and whispers to her, "I have a lot to talk to you about... later."
Shinichi then goes over how the poison was hidden in the ice, and how the woman who bought the drinks put it in both cups. Her own drink didn't poison her because she, unlike the man, didn't eat the ice. Later, when the officers were searching the car, she dumped her drink outside, but Shinichi retrieved the ice cube. The guilty woman says "It's lucky for you that it was raining, or else the ice would have melted, and you wouldn't have caught me", but Shinichi points out that there was no way she could have known not to put her cream and sweetener into her drink, as by the time she got back, it was dark, and she wouldn't have been able to tell that her drink was not ice coffee, but cola instead. She must have opened the drinks before, to put the poison in.
Caught, she repents, and spends long amounts of time (as I am doing here now) talking about the murder case, when in fact all we are interested in hearing is how in the world can there be a Shinichi and a Conan existing at the same time.
And as people are congratulating Shinichi on his return, he suddenly doubles over in pain. "Oh no! My body is returning! It's not permanent!" thinks Shinichi, and he flashes back to the hospital.
There, in his hospital room, we see Conan and Ai talking. "The third choice", says Ai, "is to take this experimental drug. It's never been tested, and it will probably kill you, but if it succeeds then you will be Shinichi again. Is she worth the risk?"
Back to the present, everyone gathers over Shinichi, writhing on the floor in agony, and slowly, he passes out.
We see through his eyes as he wakes up. There, standing over him, are Ran, Kogoro and Heiji. He expects to be small again, when he notices that all his clothes still fit. He's still an adult. He's still Shinichi! The episode ends with him shouting for joy.