Mitsuru Higaki committed the kidnapping in order to use Haibara as an alibi witness. Mitsuru found out that her husband was having seeing another woman, and she decided to murder him in retaliation.
In order to faciliate the deception, she purchased an appartment near the airport and decorated it identically to her own living room, thus creating the illusion that she and Haibara were held captive in her home, which would be too far away for her to get to the airport and commit the murder. Since the appartment was very close, Mitsuru was able to use the five hour interval in which Ai Haibara was unconscious to fly to Chitou, murder her husband and return to transport Haibara back to her own house.
The decisive pieces of evidence are:
the fact that the wine delivery man rang the doorbell to Mitsuru's appartment six times in rapid succession, but Haibara heard the bell ring only twice, and at a much slower pace;
the floor in the fake appartment has a shifted floor. Conan stumbles upon that clue after Haibara remembers the odd way the soda can on the table rolled around as she was chloroformed the second time.
Season 24 (2019)