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.
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.
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.
On Thanksgiving, Team Scorpion’s new neighbor 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. Toby works with Cabe to uncover the details of his father’s death that he has suppressed since he was a boy.
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 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.