I think that the final episode will go along the lines of:
Conan and Haibara figure out the BO boss location and agasa sets up a tracking system and bugs conans clothing so that if he is killed, his location is instantly broadcast to all police stations.
Next, conan and haibara infiltrate the building, and discover:
>Agasa is the BO boss<
Right when they figure it out, he says: "Thats right, im the boss of this organization. Ive been helping you only to better us and train us. The other is because i knew you before this all happened and felt sorry for you."
Next, Conan and Haibara will be surrounded by other members, Gin and Vodka. However, Vermouth this jump in and shoot and kill Agasa, while Gin and Vodka try to gun down Vermouth, but fail. She escapes.
Conan and Haibara then run into the labs to find the Apotoxin cure. They then find it. Right when they do, Haibara is shot and wounded by Gin.
Conan tries to save her, but she is then killed by Gin to rattle Conans bones.
Conan then runs into the hall and notices bright light coming from the doors. He opens them, and the entire tokyo police force is outside. Gin and Vodka are caught. However, right as they are caught, vermouth turns and kills Conan.
-However-
Shinichi wakes up in a medical center. He looks around and his doctor is Araide. Ran and Kogoro and standing over him, Kogoro with his grim face and Ran all happy. He comes to find out it was all just a dream. After he was drugged by Gin the killing failed, but instead of Shrinking like in his dream, he only was in a coma. He discovers that he was in a coma for 5 years. He is now 22 years old and so is Ran. He never met Haibara, Heiji, Ayumi, Mit or Genta. Agasa is still close to him (Unlike the end of his coma dream).
He then gets out and ran and him confess feelings. Right after, Shinichi is shot randomly out of nowhere and they run into the hospital. The black organization is targeting him because the killing failed. Right after he was shot, he breaks away from Ran and escapes into the city. Ran is then drugged by the same drug and turned into a child. She panics but comes to relize she cant be found or she will put Shinichi at risk. The events of Shinichi`s dream are now Rans reality.
The final scene says: "To be continued", and the show spins off as "Ran Mouri- Detective".
An epilogue is shown and says for the following characters:
"Ran mouri is now a child and targeted by the BO, she must use her skills and wits to survive in the dark world"
"Shinichi was killed later by the BO and was buried in America, where his parents are."
"Agasa never got over the death of Shinichi and left Japan. He went to Europe and became a popular Ballerina"
"Haibara is still part of the bo as Shiho. Instead of like conans dream, she is a very cruel woman who grins at the pain of others. She is involved with Gin, and is high ranking"
"Sonoko was sad that Ran went missing. She dropped out of Design School and traveled to Spain, where she became an actress"
"Chiba was hit by a bus while crossing the street. However, his fat protected him. Only the bus was damaged."
The end.
Lol