The Obama regime was coming after General Michael Flynn for a couple years before he signed onto Team Trump, with their obvious policy differences after dismissal by Obama in 2014. His military career ended when Obama dismissed him as defense intelligence chief. Flynn claimed he was pushed out for holding tougher views than the Obama administration about Islamic extremism.
Once on Team Trump, the very certain revelations would have surfaced quickly within the camp, and that would have meant a great disturbance in the Force for the Won, which led to the warning that Obama made to Trump about hiring Flynn.
Ultimately they were after him for his book Field of Fight regarding Iran and the Obama admin cover up of the documents found on the bin Laden raid concerning AL Qaeda and Iran, including training Iran was providing to terrorists. The admin was hiding the discoveries from the public and apparently from congress too because they were trying to normalize relations with Iran.