The CIA hires Team Scorpion to track down a missing spy plane, and the CIA is willing to pay. The search leads them to Area 51. When they find the plane, the team gets a new mission with a higher payday. They have to figure out where the plane was going and stop the pilots from kidnapping an employee of Area 51.
Happy, Toby, and Paige break into Area 51 to find the expert, but they are captured by Area 51 guards. When they take the guards to the secret spy plane to verify their story, they discover that the plane is gone. Cabe and Walter are hiding onboard. Happy, Toby, and Paige are put in lockup.
Megan isn't doing so well. She developed an upper respiratory infection which is particularly bad for someone with MS. The doctors are saying she only has weeks left. Team Scorpion doesn't take it well, and Cabe and Paige work on getting them to process the severity of Megan's situation. Walter's currently banking on being able to save Megan's brain in some sort of machine that hasn't been invented yet.
Walter and Cabe manage to take control of the plane, and Happy helps them to land it safely in the dessert.
CIA tells Team Scorpion that they dug around too much into this plane.