I've been thinking lately about Vermouth's secret. What could it be that she lets Amuro blackmail her? Even if she caused Amuro's death or not, the secret will still be leaked. So, indirectly she's supposed to protect him. And, does she not get curious how was he able to get this info and whom or what is he checking in with? If whom, she can imitate his voice right? not just his voice, she can check in for him personally or change the setup.
And that leads me to think that Vermouth is interested in Bourbon, I mean his theories. He's supposed to hunt Sherry. And Vermouth wants her dead, well before, but she made a promise already. So when the two of them 'succesfully' captured Sherry, Bourbon learned that Vermouth wants her dead by those bombs. Vermouth's secret. Sherry dead. Maybe Haibara knows something.
Still on theories, Vermouth is rebutting Bourbon's theory about Akai's death. She could have already known Conan's ability to plan ahead when he faked Haibara's death. Either she wants to mislead Bourbon's investigation or she's just testing the theory, or she really believes that Akai is dead.
She has an inkling that Kir is a spy, maybe she smells Bourbon is a spy too. Other than being vague at letting Conan destroy the organisation, what a plot twist it is if Vermouth's also a spy. Hahah. But on the issue, She suggested Bourbon should probably stop doing as he please since she says that Gin wants to do something about the rats. Did she just warn Bourbon?
And speaking of spy, Kir texted Akai about RUM in a hurry. Maybe she's already cornered by this time by Rum?