The new Director of Homeland Security, Adriana Molina, reunites the team when a nuclear powered Russian satellite is knocked out of orbit and must be diverted before it detonates over Southern California. Paige and Walter face their feelings for each other when hospital footage reveals that Paige kissed him.
Team Scorpion heads to Cuba when a woman from Cabe's past pleads for him to help catch a Serbian war criminal.
In order to save the lives of three judges, Sylvester goes undercover in a federal prison but Team Scorpion must break him out when his life is threatened. Alana De La Garza returns as the new head of Homeland Security and Kevin Weisman returns as Walter's new friend, Ray, whom he meets doing his court-mandated community service.
Walter, Cabe and Happy are trapped with the crew in a top secret submarine when an explosion sends it to the bottom of the ocean with limited oxygen and a self-destruct function that will soon activate.
Team Scorpion goes undercover on the "Super Fun Guy" movie set in Kazakhstan in order to disable a soviet era nuclear missile being sold by terrorists.
Walter's attempt to "normalize" goes horribly wrong when a nefarious virus is uploaded to his computer, turning Team Scorpion's new "smart" building project into a burning death trap with people locked inside.
Team Scorpion must stop a sabotaged runaway subway train with Paige and Ralph on board. Also, in his attempt to impress Happy, Toby has his first boxing match.
Team Scorpion helps the CIA locate a top-secret aircraft in Area 51 in order to raise money for Walter's research to save his sister's life.
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.
When Team Scorpion and Walter's parents visit Megan in the hospital as her health deteriorates, they are quarantined after a deadly fungus outbreak threatens to infect everyone.
Team Scorpion goes undercover at a university to find a hacker who infiltrates the Federal Reserve and threatens to collapse the world economy.
Team Scorpion must stop a catastrophe on Christmas Eve when heavy rain creates a large crack in a dam, putting an entire town in danger.
The members of Team Scorpion brave subzero temperatures in Antarctica to save a United States Special Forces unit; Toby risks his life to save Happy.
Sylvester comes face to face with his estranged father, a retired general, who asks Team Scorpion for help when he believes that a dictator in Africa has uncovered a deadly World War II-era weapon of mass destruction and intends to use it.
Team Scorpion is tasked with helping NASA's top secret rocket launch, but they must sabotage their own mission when Walter's date from the previous night has a bomb strapped to her chest.
After a powerful earthquake hits Los Angeles, Team Scorpion need to make sure that a pinched gas line does not cause a huge explosion.
While Team Scorpion works to stop an influx of drugs being smuggled into the country via drones, Walter gives Happy and Toby an ultimatum on their new relationship.
Sylvester appears on The Price Is Right and wins big time. The team need to infiltrate a high-end car smuggling operation that is getting ready to import weapons to South America.
When Los Angeles' blood supply is hacked and deemed unusable because of fear it's been tainted, Team Scorpion must find the culprit in order to save a young girl in desperate need of a heart transplant.
While on a secret mission in Djibouti, Africa, with his new Homeland protégé, Tim Armstrong, Cabe is captured and Team Scorpion must save him.
Team Scorpion's mission to recover the remains of fallen Marines in Vietnam is threatened along with their lives when a deadly tornado heads directly towards them.
Team Scorpion is hired by the Department of Defense to break into Fort Knox and "steal" a precious artifact in order to test their security, but they must break in a second time when they find something dangerous hidden inside the object.
Team Scorpion goes to Chernobyl to repair the decaying nuclear reactor before a catastrophic meltdown, but must also save Sylvester and Paige when they become trapped inside.
Team Scorpion must outthink their unstable ex-Scorpion member, Mark Collins, after he kidnaps Toby and threatens to hug him unless his cunning demands are met.