"Michael Flynn was under FBI investigation earlier than previously thought, according to a little-noticed section in Special Counsel Robert Mueller's report -- and the former national security adviser's brother told Fox News exclusively this week that the revelation suggested a long-running, high-level effort to "trip him up" and "trap" him.
Buried in the second volume of the Mueller report was a mention of an existing FBI investigation of Flynn "based on his relationship with the Russian government," which predated Flynn's phone calls during the presidential transition in December 2016 with then-Russian ambassador Sergei Kislyak that ultimately led to his termination for lying.

It was previously thought that Flynn’s communications with Kislyak – picked up by the U.S. intelligence community – made the FBI suspicious, sparking the Flynn probe."

I'm guessing but I think they were going to try to flip Flynn and use him as a spy against Trump. That is the usual MO for this type of operation.
If this was not the goal, shy wouldn't they inform Candidate Trump and them President Elect Trum and then President Trump of the investigation of one of his top sor soo to be top aides? They wanted more than Flynn. they wanted Trump and would do anything to get him.