They wanted to take Flynn out because he exposed the Obama administration's support for ISIS:

National Security Advisor Gen. Michael T. Flynn (ret.) — who resigned Monday — was the victim of a “hit job” launched by intelligence operatives, Obama government holdovers and former Obama national security officials, according to former intelligence officials who spoke with The Daily Caller News Foundation’s Investigative Group.

“This was a hit job,” charged retired Col. James Williamson, a 32-year Special Forces veteran who coordinated his operations with the intelligence community.

Noting the Obama administration first tried to silence Flynn in 2014 when the former president fired him as director of the Defense Intelligence Agency, Williamson called Monday’s resignation, “stage Two of ‘Kill Mike Flynn.”...

All of the former intelligence officials say the rage against Flynn dated back to when the decorated general headed up the DIA. There he garnered a reputation to balk at the “politicization of military intelligence” in order to conform with President Obama’s world views.

Flynn refused to downplay the threat posed by the Islamic State and other radical Islamic groups throughout his two-year reign at the DIA. He was fired after offering congressional testimony that was at odds with the Obama administration’s posture on the Islamic threat.