While all evidence pointed to Iran, Will spent this finale trying to prove that Truxton and Atlas-McDowell was behind the oil tanker explosion.
Katherine came across evidence that would help, as her husband and David recorded a message on the Meet Me in St. Louis DVD. But just as Katherine was meeting Will in the park to hand it over, she was injected with something and killed. We also learned that Andy had been working with David all along, as she accompanied Katherine to the park and then quickly exited the scene before Will could find her.
Will also confided in Miles about the conspiracy and the two of them worked to bring Truxton down. They ended up using Hal to hack into some computer and find evidence that connected Donald Bloom to Spangler and everyone else. Will confronted Spangler with this information and with his report, but the boss remained cocky and unaffected.
That was mostly due to the fact that his friends pretty much planned to kill him. He received an envelope earlier in the day and the final scene was of Will letting Spangler walks into API and looking at what he left on the edge of the roof, what had been in the envelope: a four-lead clover.
Elsewhere: Spangler promoted Grant to team leader and Tanya resigned.