So what did happen?
Vermouth died in the falling (literally) of the main Black Organization hideout
The mysterious Anokata turned out to be Miyano Shiho's father (think about it, he fits the hints Gosho Aoyama gave us about Anokata)
Anokata was killed by Gin in friendly fire, (the identity of Anokata was discovered by our side only after his death)
The rest of the Black Organization (including Spider) were arrested by the CIA
The Shounen Tantei-dan were semi involved in that Genta, Mitsuhiko, and Ayumi chose to follow Ai, Aya, and Conan into the building, and were the ones who contacted Mouri Kogoro (who was followed by Eri, Ran, Heiji, Saguru and Kaito for some reason), and the Metropolitan division One, who in turn contacted James Black and the FBI, Genta, Mitsuhiko, and Ayumi were saved from being crushed in the building colapse by the joint effort of Shinichi, Hidemi, and Ran.
At some point Ran meets Conan after just being forced the APTX antidote by Ai, and watched Conan transform into Shinichi
Ran spent some time yelling at Shinichi while they found some clothes for him in a random room, forgiving him later in the hospital after Shinichi took a bullet from Gin for her
Shinichi and Ran get their full confession to each other and are officially dating
Shinichi and Heiji discover Kaito's alternate alias as Kaitou Kid, but vow quietly to keep it a secret until after Kaito finds the Pandora and they are able to catch him in action, otherwise the Heiji, Shinichi, Kaito, and Saguru become close friends (near death experiences can do that you know)
Eisuke follows the FBI in hopes to find his sister
Eisuke is forced to take APTX by Gin
APTX Eisuke saves Aya from falling to her death at some point, love blossoms between the two
Conan/Shinichi returns to Shinichi for good, Shiho/Ai stays as Ai, APTX Eisuke is stuck as a child due to how the antidote would react with his blood type, Aya/Akira choses to stay as Aya because she does not want to leave the Shounen Tantei-dan or Eisuke
The destruction of the building is reported to take the lives of Edogawa Conan, Miyano Shiho, Hondou Eisuke (seventeen year old version), and Kudo Akira
The CIA give Aya, Ai, and Eisuke paperwork to match their persona's, and officiate the deaths of Conan, Akira, Shiho, and seventeen year old Eisuke
Hidemi is documented to be the mother of APTX Eisuke and named him after her absent brother, with the father's name said to be unknown, child Eisuke took Hidemi's last name, which is how teen Hondou Eisuke became the Hondou Eisuke the son of Hondou Hidemi
Kudo Yusaku and Kudo Yukiko invite Hidemi and Eisuke to live with Shinichi in the house in Beika
Aya is given permission to stay with Shinichi, Hidemi, and Eisuke in the Beika house
Edogawa Fumiko (Conan and Aya's mother) and Edogawa Fenji (made up name for Conan and Aya's father) are coming to the memorial of their son (well, two FBI agents dressed up as Fumiko and Fenji are coming to the memorial)
A memorial is planed for Conan, Shiho, Akira, and Eisuke