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.
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.
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.
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.
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 festival's historical inaccuracies.
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,
Team Scorpion takes a case on Halloween 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. Meanwhile, Walter considers taking note of Paige's interests to benefit their relationship.
A simple accident while decommissioning an old nuclear missile causes Team Scorpion to be exposed to toxic vapor. But they must endure it to prevent the nuke from detonating. Meanwhile, Paige confronts Happy about constantly tagging along with her and Walter.
Team Scorpion continues to work with their nemesis, Mark Collins, to prevent an extinction event that could end humanity. Meanwhile, Cabe's last-minute decision on the case leads to the possible end of his career.
Season 4 begins with Team Scorpion being forced to work with their old nemesis Mark Collins in order to prevent the extinction of mankind. Meanwhile, Walter and Paige awkwardly navigate their new relationship.