Imagine a potential terrorist threat threat to the United States involving WMDs and to uncover the plot and stop it before thousands are killed the government dedicates 2 agents to the case! The FBI has over 10,000 special agents. DHS has many more. I would expect that in a case like this the FBI would dedicate at least hundreds if not thousands of special agents along with all kinds of surveillance resources, state and local police and who knows what else.
But in this show we have a threat of a chemical weapons attack and our hero captures one of the bad guys. But since there are only 2 people from the government involved. One has to go investigate an possible clue while the other is left alone to watch the prisoner - for hours and no backup or other resources arrive to help!. This is laughably stupid.
On top of that, the two legitimate agents, if you can call them that, involve a young female programmer in their plot and expose her to top secret information without vetting her through a typical background check. Just think if this thing goes sideways. Imagine the investigations and the reaction to the fact that this amateur was deeply involved in the plot. The two agents involved would be destroyed, imprisoned and then destroyed again.