Season 3

1. Civil War

After both of their personal and romantic issues fail with Paige and Happy, Walter, Toby, and the rest of Scorpion put their plans on pause as they work with the U.S. Navy to stop two out of control fighter jets taken over by hackers while flying over Los Angeles, targeting their weapons at each other. The hackers also cyberjack four U.S. destroyers and position the ships 300 yards (274 m) outside Miami, Boston, Portland, and Long Beach with high explosive BGM missiles pointed at the cities. This forces the U.S. military to ground all planes and shut down the nuclear missile silos, leaving the country defenseless.

The hackers are back-traced to Bulgaria. Happy and Toby successfully help the Navy regain control of the remaining fighter plane after the hackers use it to shoot down the other. However, Walter and Paige are unsuccessful at hacking the hackers' signal and are almost killed trying. Meanwhile Sly, Cabe, and Tim travel to Sofia, Bulgaria in a Valkyrie to find the hackers, where Sly shows off his card counting skills to get the attention of a crime boss they need to find the hackers.

2. More Civil War

After Sly gains the attention of a crime boss, he must help him win back millions from a Chinese rival in exchange for the address of the hackers. The others successfully regain control over the destroyers, only to find out there is also a nuclear submarine under the hackers' control. They try to use magnets to disrupt the hackers' signal, but are mere seconds too late in implementing their solution. Cabe and Tim run into a trap, eventually managing to find the hackers' lair, but not before the hackers launch a nuclear missile.

In a team effort, Walter reprograms the rocket's GPS to disable it. Meanwhile, Sly accidentally loses the game. After the crime boss finds out Sly works for the U.S. government, he decides to kill him. On the way to a secluded area, Sly escapes and is ultimately rescued by the Valkyrie pilot. Later, on Cabe's advice, Walter must face the reality that he is not emotionally ready for Paige, deciding to make amends with her and Tim.

3. It Isn't the Fall That Kills You

Tech mogul Richard Elia returns to hire Scorpion to help his company with their first crewed space launch, with a deadline with NASA looming. Walter's rocket throttle design seems unstable, so he runs diagnostics on it. While working on the rocket, a lightning strike launches Walter into space. Due to several malfunctions, including low oxygen, he starts to hallucinate that Paige is with him in the rocket capsule. The team must figure out how to save Walter before his oxygen runs out in less than 30 minutes, all while dealing with the uncomfortable situation. They turn to the Russian Federal Space Agency for help in return for giving them credit for saving an American citizen. Walter and Toby devise elaborate plans to deal with their loves while at the garage.

4. Little Boy Lost

After Ralph's friend Daniel, a non-verbal autistic boy, goes missing during their school field trip, Scorpion searches for him only to find that a suspicious man took Daniel's voice tablet mistaking it for his intended dead drop. They soon discover that the tablet is linked to the S6, an international mercenary ring. The team races to track Daniel before the S6 do, but arrive too late and then must save a panicked Daniel. He reveals that he opened a file on the wrong tablet, detailing an assassination plan to use smart bullets to take out a candidate running for Senate.

They work together to stop the plan, succeeding thanks to Happy's quick thinking. Toby visits Mark Collins in prison to ask him about Happy's husband and, instead of an answer, he gives Toby a riddle. Later, he finally figures out the riddle and finds out the identity of Happy's husband: Walter. Happy reveals their marriage was purely to help Walter get a green card and then reveals that she is pregnant, requesting a divorce from Walter.

5. Plight at the Museum

Scorpion is hired by L.A.'s Natural History Museum to determine why an ancient pillar is rapidly decaying and must stay overnight during lockdown to solve the problem. The simple mission turns complex when a group of Aldorrian thieves infiltrate the museum, wanting to steal tantalum-181 from an asteroid on display in order to enhance a nuclear bomb. Meanwhile, Toby panics about becoming a father and Paige gives him some parenting advice. Later, a hard-nosed case worker from USCIS shows up and is curious as to why Walter and Happy have been living at separate addresses for the past six years. This causes Toby to give them behavior lessons.

6. Bat Poop Crazy

Scorpion travels to a remote location in Wonder Rift, Arizona, where they go spelunking into a deep cave system in an effort to save a disease-ridden bat population from harming the North American ecosystem. In order to prevent the spread of White Nose Syndrome, they must aerosol fungicide into the cave after they meet up with two zoologists. They end up having to save the scientists after the bats become aggressive and attack them. Meanwhile, Happy stays at the garage running comms and has to look after a hyperactive Ralph who is on a sugar rush from eating too much candy. Later, the team throws a Halloween party and wears costumes to help Happy and Walter with their impending immigration inspection by strict agent Joyce Linehan.

7. We're Gonna Need a Bigger Vote

Scorpion gets a mission directly from the U.S. President and works with the FBI on election day when hackers try to crash the voting servers in the latest U.S. presidential election. Since Walter is flagged by immigration as a person of interest for citizen fraud, he cannot help the team. Undeterred, he partners with Ralph to find out that the Chinese consulate and their ambassador are behind the vote hack as a means to gain control of international shipping lanes. Later, Paige goes with Tim to the Veterans' Ball and has to meet his parents.

Meanwhile, Agent Linehan visits the garage and, although she knows Walter and Happy perpetrated a fraudulent marriage, is forced to grant Walter his citizenship after Washington, D.C. enacts a private bill as a reward for his work on the case. Happy finds out she was not pregnant, her blood test a false positive caused by contracting cadmium poisoning after working on the solar panels, but she and Toby do get properly engaged.

8. Sly and the Family Stone

Most of Scorpion escorts Walter to his hometown in Ireland to help his parents with the blessing of Megan's cenotaph on Pattern Day for her one-year remembrance memorial. Toby stays at the garage to aid Happy with her chelation treatment and convince her to have a big wedding. Meanwhile, the Irish tradition is broken when Walter discovers the nearby lake is about to erupt, which would result in a poisonous gas cloud of carbon dioxide threatening the entire village. Cabe and Toby, via cell phone, try to ease the tension between Walter and Tim, who must work together to save the townsfolk. Also, Walter makes amends with his childhood bullies by fighting them, earning their respect.

9. Mother Load

Paige's Thanksgiving dinner for the team is put on hold when her estranged con-artist mother Veronica ( Lea Thompson ), posing as a real estate investor, enlists Scorpion's help after she accidentally discovers a forgotten radioactive nuclear reactor that is about to explode in an abandoned building. In addition, she is being hunted by shady businessmen who want their money back. Wanting to save his beloved Warlock's Chest comic book store from demolition, Sly starts a petition and decides to run for town alderman. Meanwhile, Cabe becomes interested in Allie Jones ( Reiko Aylesworth ), the competition's campaign manager. Later, Veronica, after reading Walter's good intentions, declares that he is what is best for her daughter, not Tim – and that she will help him get her back.

10. This Is the Pits

Scorpion must act quickly with LAFD Fire and Rescue after a woman runs off the road to avoid a cyclist and gets trapped in her car at the bottom of the La Brea Tar Pits. Also, Sly and Cabe fail to raise enough money for Sly's campaign to run for alderman of West Altadenia, leading Veronica to teach Ralph how to make a bigger profit by selling his Forestry Brave cookies as ice cream sandwiches to hipsters and, instead of keeping the conned money, they give it to Sly as a campaign donation. Later, Walter ends his partnership with Veronica, feeling the deceit would eventually hurt Paige. Tim declines a security job offer in Amman, Jordan in order to stay with Paige and continue helping Scorpion, this time with a permanent position.

11. Wreck the Halls

Scorpion spends Christmas Eve at a cabin free of all electronic devices, cell reception, and Wi-Fi. But it is not a team holiday without a problem. While out searching for a Christmas tree to cut down, they encounter gunrunners in the woods holding an ATF agent hostage. The team is discovered at their retreat and sets up homemade traps to take down the criminals. Even though their plan works, the agent is really a part of the gunrunning gang and captures Ralph. Paige and Walter race after him and rescue Ralph. Later, Tim and Walter have a heated argument over Paige, causing Tim to rethink his position as a full-time member of Scorpion. In the end, he decides to take the security job in Amman, but Toby tells Walter that Paige will blame Walter for it.

12. Ice Ca-Cabes

Scorpion is back to normal with the regular roster after Tim's departure, but Paige is upset about how Walter handled the situation and just wants to focus on work. Meanwhile, Cabe is moving out of Happy's home and she is actually sad about it; he gives her his mother's brooch to wear on her wedding day and she considers him a friend. The team's routine mission at the Federal Pumping Station in Redwood, California in the desert turns into their hardest case when they are forced to freeze Cabe's body in order to save his life after he is seriously wounded by a copper shard that snapped off from the force of the turbine's friction.

The team must collect various materials, forcing Sly and Happy to face their fears and Paige and Walter to enter a nudist spring. Later, at the hospital, Walter finally expresses his feelings for his long-time fatherly friend and tells Cabe he loves him.

13. Faux Money Maux Problems

Scorpion takes a private job revamping a winery's viticulture technology with selective harvesters and optical sorters. On the way to the winery in a limousine, the team is knocked out by kevloturane, a subtle but potentially lethal gas. They are tricked by a foreign diplomat posing as the vineyard owner, and she forces them to make American counterfeit money for her country, the fictional Norteguay of which her brother is dictator, that intends to ruin the U.S. economy. After being locked in a warehouse with her mother, Paige has to rely on her mother's con-artist skills to save them all. Meanwhile, at the winery, Toby and Happy are followed by a Norteguaian henchman and escape to the garage to help the rest of the team, who believe they are out of the country but are really in Simi Valley, California.

14. The Hole Truth

Scorpion is hired by the US Army Corps of Engineers to help a sandhog unit locate a leak in a municipal water line. The micro leaks they find cause the soft soil to create a massive sinkhole that is ready to swallow up a silo filled with chemicals, along with a worker trapped on top of it. If this happens, the drinking water supply of one of Southern California's most prominent aquifers will be tainted. Meanwhile, Toby and Happy have to help Walter, who is slipping down their "EQ" scale, as he has been too sharp and insensitive to people's emotions ever since Paige decided to leave him to his own devices.

Paige also has to help Veronica get back the con money she buried at the abandoned factory where they found the nuclear device, which is now being worked on by a demolition crew. She devises a cunning plan for her mother to cheat the men who want her to pay for her sins; however, it forces Veronica to part ways with Paige for good. She leaves a large cache of her dirty money to Paige in Ralph's name.

15. Sharknerdo

After Scorpion loses a contract with the Department of Energy to upgrade their server when Walter disagrees with a rep over their "mathematically inaccurate" fee, he takes on a case to use their echolocation tech in search of pirate treasure. The team is hired by a Marine salvage company that believes they've found the San Caldera, a Manila galleon that sunk by Drakes Bay in 1595 carrying a fortune in gold. Meanwhile, Allie helps Sly out with his campaign by getting him an interview with a teenage reporter for the West Altadena Shopper.

However, he has more important matters to attend to when he has to help rescue Walter and Paige when they're stranded in the middle of the Pacific Ocean after their boat explodes from an electrical problem. Even though they're able to make it to a Danish buoy to get out an S.O.S., a frenzy of sharks surrounds them.

16. Keep It in Check, Mate

Scorpion gets a case from the Eastern European Desk of the CIA when two informants in Sardovia are murdered. In order to get close to a Sardovian asset, Walter and Sylvester enter an international chess competition undercover in an effort to extricate the spy/ chess grandmaster before her identity is exposed by code breakers. Meanwhile, Cabe works with the FBI to convince Happy's father Patrick to testify against Sonny Dubin, a man who ran a stolen car ring to move drugs across the border for whom Patrick used to illegally wipe off VIN numbers of vehicles that he brought him at his garage.

In order to take advantage of the deal Cabe has struck, he has to self-surrender and will be imprisoned for two years, causing Happy heartbreak. Later, Ralph is asked to the Valentine's Day dance by two girls and goes to the men for advice instead of Paige, who is disappointed since emotional problems are her specialty. However, he comes to her wanting to learn how to dance.

17. Dirty Seeds, Done Dirt Cheap

Scorpion travels to Greenland for a simple job, repairing a malfunctioning system at the Granse World Seed Vault. When they become trapped in high humidity rooms, Happy, Sylvester, and Cabe have life-threatening psychotic hallucinations due to ergot spores, which affect the fear center of the brain. Happy relives her childhood rejections waiting to be adopted, Sly believes he will catch a disease from chickens, and Cabe believes he is too old to date Allie, who is 15 years his junior, and turns into an arthritic old man. Meanwhile, Paige, Walter, and Toby, who are not infected, try to help them overcome their worst fears over their comms. Later, Sly must overcome his fear of public speaking to win a political debate against his opponent, who tries to use a bullying tactic on him.

18. Don't Burst My Bubble

When Happy's new online friend Ada, a teenage girl she met on a website for female mechanics, doesn't respond to a private chat, Happy heads to Ada's hometown of Lancaster. She enlists Scorpion to help her move Ada, who has a severe immunodeficiency brought on by aplastic anemia, and the sterile bubble that protects her weak immune system to a germ-free location after a severe storm leaves her home surrounded by dangerous debris. Meanwhile, Walter tries out his newfound emotional state on Paige when she and Tim break up after he decides to accept an eight-month contract extension in Jordan.

Later, Sly loses the alderman election after Allie's boss and Sly's opponent forces her to post a photo on the internet of the germophobic Sly shaking hands with a veteran and wiping his hand afterwards. This causes Cabe to break up with Allie, although Sly nonetheless manages to save the Warlock's Chest from being condemned by qualifying it as a historical landmark. Also, the team holds a Winter Formal and uses a virtual reality headset designed by Walter to allow Ada to experience the dance.

19. Monkey See, Monkey Poo

Scorpion works with the World Health Organization to stop the dangerous Marari virus from spreading throughout South America and causing a pandemic. They travel to the Amazon rainforest to locate an endangered monkey species called the Homboldt Capuchin that may have the antibody for the cure. Meanwhile, in order for their marriage to work, Happy wants to express herself better, so she drags Toby to see "quack" therapist Dr. Cecil Rizzuto ( Penn Jillette ) for premarital counseling. Later, Walter identifies with Cabe's emotional pain from losing Allie after his own heartbreak over Paige and actually shows some empathy towards him.

20. Broken Wind

Scorpion is hired by the Department of Energy to design a special graphene alloy turbine to upgrade their experimental blade-less windmills at a wind farm in Energy Valley. When Happy and Paige get stuck in a gondola, the rest of the team races to save them after the cable supporting it snaps. The men make it hard for Toby to decide on a best man for his wedding, resulting in him asking Paige to be his "best ma'am." To avoid a similar competition, Happy declares them all her "dudes of honor." Additionally, Sly earns the Stone of Valor at The Knights of Altadenia vesting ceremony and wants a reluctant Cabe to join in being knighted into his clan after his contributions towards saving The Warlock's Chest.

21. Rock Block

Scorpion is hired by the government of the fictional Hechnyan Republic to retrieve a space capsule carrying an asteroid, but discover it contains DNA strands that may have deadly pathogens capable of killing millions. During the mission, Allie visits Cabe, who stayed behind, to inform him that her boss will be stripped from his position as alderman for accepting bribes and that Sylvester will be able to take his place. Sly initially rejects the offer, instead offering Cabe a trade; he will take the oath of office only if Cabe takes Allie to dinner.

Happy and Toby secretly take advantage of freebies from reception venues while Paige struggles with her "best ma'am" duties. When she discovers their secret, they offer her a bribe from their haul. Later, things heat up for Walter and Paige when they see if the song Walter picked out for the wedding is suitable for dancing.

22. Strife on Mars

Scorpion is hired by Kapper Aerospace Industries in Solvang to fix the thorium power grid in their Mars simulation biodome. When a critical system fails, they must extract a pair of scientists who have been living inside for 11 months. Also, Walter and Paige plan out their own versions of Toby and Happy's Jack and Jill Bachelor/Bachelorette Party: Walter with a trip to the science center, a planetarium, and the natural history museum, Paige with a party bus and look-a-like piñatas. Meanwhile, the couple prepares to move in with each other, quickly learning that they have different styles and ways of living.

An oxygen-ozone mix in the dome triggers Walter's memory of the earlier rocket mission and he discovers what really happened in space with Paige. Later, realizing Paige played him, Walter fires Paige at Scorpion but does so only after landing a position for her with Richard Elia; Paige however tells him to "go to hell" and leaves with Ralph.

23. Something Burrowed, Something Blew

On the day of Happy and Toby's wedding, Scorpion gets a case in Wyoming when lightning strikes set fire to an underground coal mine. They must extinguish the fire before it destroys a telecom cable, but they need to be back in San Jose, California in time for the ceremony. When complications arise and they don't make it, Paige plans an impromptu wedding at Kovalsky's Diner, their favorite greasy spoon, and gets Ray, who's an ordained minister, to give the vows. Walter expresses his feelings for Paige, stating the reason he fired her is because he's in love with her.

To his surprise, she feels the same way and they share a not-so-intimate moment. Later, Cabe gets a call; the French Polynesian governor needs help setting up their underwater wave-powered generators and they're willing to fly the team out to Tahiti. Looks like the newlyweds get a free honeymoon. However, on the private flight, they hit some turbulence and, with Happy as the co-pilot, the plane starts to go down.

24. Maroon 8

On the way to Tahiti, the team's plane crashes on a deserted island after a battery in one of the wave-powered generators explodes, causing shrapnel to cut the plane's hydraulic lines. Everyone except for the pilot, Scotty ( Rockmond Dunbar ), is unharmed. Scotty is suffering from crush syndrome and will die if freed. The team rushes to build a makeshift dialysis machine out of the wreckage to save him, while also trying to find a way off the island. In the meantime, Sylvester's near-death experience instills him with a new surge of confidence and Toby learns some surprising secrets about Happy's past.

They found the old Japanese bunker from the Pacific War in World War II, as Sylvester will try to translate to Japanese language on the old Japanese radio. Also, an overeager Walter struggles with his emotions while adjusting to his new relationship with Paige and Ralph is worried the relationship won't survive long on the island.

25. Scorp Family Robinson

Three weeks after crashing on a deserted island, the team is divided on plans to get rescued before the monsoon season, so the team splits up. Walter thinks a magnetic field change can get them home, while Toby tries to make a raft out of newly discovered oil drums. Meanwhile, a long-bearded Sylvester is losing his mind in the bunker with his pet chameleon. Everyone works together to rescue Ralph and Scotty when they are smothered in a sand pit created by an exploding copper wire experiment that results in an electrical disturbance, signalling a plane to fly above them. They spell out SOS on the sand and are saved. Back home safe, Paige and Walter are finally left alone and they consummate their relationship.