You need to collect clues to help you narrow down the suspects. These clues are used in campaign capers, and you can obtain the clues you need by playing the caper! You discover them while you are walking around a level, after solving puzzles such as hacking into a phone or cracking open a safe, and completing mini-games such as grappling through streets in pursuit of a VILE agent. 
If you're in the ACME Files, the people you encounter might have clues for you. Just continue talking to them, or try to ask around to see whether anybody else has further information for you. Occasionally, you'll encounter puzzles to solve that will reveal clues, too. 
If you've already narrowed it down to a few suspects and are still indecisive, you can view your suspects' dossiers and then do a "Confirm Recon" to confirm for yourself whether their alibi is true or suspicious.