Team Scorpion must work with their old nemesis Mark Collins in order to prevent the extinction of mankind. Also, Walter and Paige awkwardly navigate their new relationship.

When poachers almost kill a pregnant endangered deer, Team Scorpion recreates the animal’s womb to try to save it and its baby’s life. Also, Happy and Toby discuss the future of their family.

While decommissioning an old nuclear missile, a simple accident causes Team Scorpion to endure exposure to toxic vapor while trying to prevent the nuke from detonating. Also, Paige confronts Happy about constantly tagging along with her and Walter.

While attending a tech convention, Team Scorpion is taken hostage by a group attempting a virtual heist.

At Halloween, Team Scorpion takes on a case to prove the existence of ghosts on the Queen Mary but find an all-too-real disaster when they locate a “ghost ship” on a deadly collision course. Also, Walter considers taking note of Paige’s interests to benefit their relationship.

While tracking a device that can prevent a nuclear meltdown through the Los Angeles sewers, Walter learns the nuances of listening and not offering advice to Paige. Also, Team Scorpion meets Florence, their new neighbor at the garage, after she sends a mix of smelly chemicals through their shared ventilation as a warning to keep the noise down.

For Sylvester’s birthday, Team Scorpion visits a renaissance festival, but the revelry is cut short when a group tries to rob a nearby police evidence locker. Also, Paige grows weary of Walter’s play-by-play of all the historical inaccuracies at the festival

On Thanksgiving, Team Scorpion's new neighbor, Florence, joins them at sea on a mission to destroy a floating island of trash, but her flawed contribution leaves her, Walter and Happy stranded on the quickly dissolving island. Also, Toby works with Cabe to uncover the details of his father's death that he has suppressed since he was a boy.

As Cabe’s trial looms over Team Scorpion, a simple case goes sideways when they help a father and his daughter whose plane crashes nearby. Also, Paige helps Walter navigate his feelings about Cabe’s possible future in prison.

As Team Scorpion anxiously awaits the verdict of Cabe’s trial which could send him to prison, they focus their nervous energy on trying to save a dog stuck in a cistern.

On Christmas Eve, when Walter chooses work over spending quality time with his friends, he falls down the stairs and hits his head, and as he lays unconscious, he enters a dream world where Team Scorpion never existed.

Team Scorpion must work with Toby’s nemesis, Quincy Berkstead, and his wife, Amy, Toby’s ex-fiancée, when they are locked inside an artificially intelligent doomsday bunker that aims to kill them. Also, Walter is distracted by his recent dream where he is married to Florence, not Paige.

A solar storm knocks out power in Los Angeles, and Team Scorpion must help a teen pilot and his girlfriend who are lost over the Pacific without navigation or radio contact. Also, during the crisis, Walter must look after a group of Ralph’s classmates, and Cabe tries to tell Allie finally that he loves her.

Team Scorpion must prevent an incoming tsunami from hitting a vulnerable nuclear power facility, and Toby secretly helps his ex-fiancée retrieve her stolen identity.

On Valentine's Day, Team Scorpion must set aside their romantic plans to help a doctor and pilot trapped inside a helicopter that crashed atop a skyscraper. Also, Toby and Happy wait for news on their fertility results, and Sylvester realizes that he may have feelings for Florence.

The geniuses of Team Scorpion turn into knuckleheads and Paige must simplify the science for them, when their mental faculties are impaired during a job to prevent the creation of a black hole. Also, Florence and Sylvester grow closer when she helps him with a special project.

Team Scorpion inadvertently crashes a bank robbery in progress and is taken hostage. Also, Sylvester’s feelings for Florence grow.

Team Scorpion heads to the bayou to track down a cagey alligator in order to stop a deadly mosquito-borne virus, and Paige teaches Walter the concept of the “white lie.” Also, Walter hits Cabe with a tranquilizer gun and Toby must save his life, and Sylvester and Ralph help Patty when the mean girls at her school force her to get a dreaded tardy slip.

Team Scorpion must use their high IQs to win a softball game when the homeland director challenges, with all of their future government contracts on the line. Also, Walter’s secret night out with Florence puts Toby and Happy on edge.

Paige’s maternal side goes into high gear when Team Scorpion must save an unconscious, hypothermic boy stuck in the wheel well of their airborne airplane. Also, Walter’s white lie to Paige starts to take a toll on him, and Paige realizes something’s up.

Team Scorpion heads to Northeast Africa where they must carefully navigate a minefield in order to save the lives of local villagers. Also, Paige and Walter’s relationship takes a shocking turn, and Toby and Happy make an important decision.