Scorpion, minus Paige, has to participate in a training mission with Homeland Security. It does not go well. Between Sylvester's nervous break down and Happy assaulting an agent, the director of Homeland Security is not impressed. He puts Scorpion on probation. That means no cases until he approves them for duty.
When a bomb takes out a law firm and the basement beneath, Scorpion figures out there is more to this bombing than meets the eye. The family law firm was not the intended target. Instead, the bomber wanted to take out the internet for the Southeast.
Scorpion gets approved to work the case, but Agent Gallo makes it clear that this is their last chance. If they mess this up, they are done. Pressure is on Scorpion to deliver, and for Paige to manage to control them. Paige is still having trouble fitting in, so no one is rushing to listen to her advice.
After identifying the bomber, Scorpion defies Gallo's order and tracks him down. It doesn't go well. The suspect ends up in a coma, and FSG is not happy with Scorpion hindering a federal investigation.
Scorpion has to rely on evidence taken from the bomber's house to piece together a motive. When multiple bombs go off, the team finds a connection. The goal was to erase the existence of a person, but now the question is why.
While Agent Gallo and Sylvester try to take evidence to the Department of Justice, Happy and Walter work on diffusing a bomb before it takes out an entire building.