Team Scorpion is tasked with uncovering a mole inside the CIA whose judgment is clouded by matters of the heart and is being coerced into stealing deadly chemicals. Also, in preparation for the case, Paige gives Walter a flirting lesson.
Team Scorpion goes undercover on a cruise ship to locate and disable deadly stolen rockets. Meanwhile, as Valentine's Day approaches, Toby and Happy help Ralph, who is in the throes of his first crush.
A tech billionaire hires the team to rescue his kidnapped daughter. Meanwhile, feelings are hurt when Walter gives an interview and fails to acknowledge the other members of the team.
While on a mission to save lost hikers, Team Scorpion's helicopter crashes, igniting a massive wildfire that quickly closes in on them. Also, Sylvester must help their injured pilot who is unable to make it to safer ground.
To protect a key witness who is en route to testifying against a deadly drug cartel, Team Scorpion takes her on the run, with the cartel hot on their heels.
Walter learns Cabe's long-hidden secret regarding the Baghdad mission and it threatens to tear Team Scorpion apart. Meanwhile, Ralph puts his life in danger to help the team.
Team Scorpion is torn apart and uncertain about their future as a unit, but they are forced to come together to save Walter's life when his car teeters on the side of a cliff.
The new Director of Homeland Security reunites the team when a nuclear powered Russian satellite is knocked out of orbit and must be diverted before it detonates over Southern California.
In order to save the lives of three judges, Sylvester goes undercover in a federal prison. Team Scorpion must break him out when his life is threatened.
Walter's attempt to "normalize" goes horribly wrong when a nefarious virus is uploaded to his computer, turning Scorpion's new "smart" building project into a burning death trap with people locked inside.
Megan's condition gets worse. Walter starts to get frustrated about not being able to help her and in Walter's crazy quest for investors, the CIA appears in the garage with the promise of a big payday.
Team Scorpion is blackmailed to break into the United Nations to assist in the assassination of a menacing arms dealer. Also, Sylvester makes a bold move to protect Megan's wishes.
As Megan's condition worsens, the team gathers at the hospital. As they arrive, they find a pathogen has infected the hospital threatening all of their lives.
The Scorpion team goes under cover at a college to discover who is holding the federal reserve for ransom. Walter tries to help Ray, while Paige is trying to get Walter to express grief about Megan.
Its Christmas Eve and Team Scorpion must prevent a catastrophe when torrential rains create a large crack in a dam. The fight to save an entire town from the threat of it wiping out an entire town in its wake.