Season 2

1. Satellite of Love

Scorpion is back in business after new Homeland Security director Adriana Molina tasks them with a case when the nuclear-powered Russian K-12 satellite is knocked out of orbit by space debris. They race to the Rocketry Aeronautics Center to divert the now-turned A-bomb 's course before it detonates over Southern California. But after last year's car accident, Walter is not one hundred percent physically or mentally there due to a hand injury and post-concussion syndrome. His hidden feelings for Paige have also seemed to cloud his judgment. When problems arise on the job, they have to work extremely close together. Later, they test their theory of the team vs. their attraction with a working hypothesis of a kiss.

2. Cuba Libre

After a woman ( Izabella Miko ) Cabe saved in Croatia 20 years ago when she was a child pleads for his help, the team travels to Cuba for an off-the-grid mission to apprehend a Serbian war criminal who killed her family. Meanwhile, Toby gets Sylvester to confess his love for Megan by subduing his anxiety through exposure therapy. Later, not wanting to admit he was in an emotional state that led to negligence resulting in his car accident, Walter wants to plead recklessness, but may wind up in jail. However, on his lawyer's advice, Paige convinces him otherwise and he is sentenced to court-mandated community service by picking up trash in town, where he meets a new friend named Ray.

3. Fish Filet

In order to save the lives of three judges being targeted by a Japanese gang, Sylvester goes undercover in a federal prison to decipher the gang boss' codes. But when Molina refuses to help them get him out, Scorpion plans his escape when his life is threatened by an inmate. In order to break him out, Walter must work with Ray and his "Ray Way" of doing things by having his man on the inside smuggle drugs for Sylvester to take, appearing dead. Meanwhile, Ralph is getting bullied at school and takes matters into his own hands by becoming a celebrity on the news for getting accepted to multiple prestigious colleges. Later, Sylvester has a new lease on life after his "death" and works up the courage to tell Megan he loves her. Also, Toby overhears Happy making a date to meet a man at a club.

4. Robots

Happy continues to date Chet, upsetting Toby, who takes out his frustration on a punching bag. The team meets deputy director Katherine Cooper, who is now Scorpion's Homeland liaison. She tasks three members of the team, Walter, Cabe and Happy, with analyzing a "vulture" data hunter device that is attached to a communications cable 300 ft (91 m) down in international waters off the coast of California. After analyzing the vulture from a top secret U.S. Navy submarine, the vulture explodes, crippling the submarine. With limited air and no communications, Scorpion must rescue everyone on board the submarine before it self-destructs. Later, Walter proves he is not a "robot" and lets Ray stay in a trailer at the garage.

5. Super Fun Guys

The team must pose as a film crew to get onto the Super Fun Guy movie set in hopes of locating a Soviet 1970s-era nuclear missile that is being sold by arms dealers on an old military base in Kazakhstan. To sneak past the armed-guards, they must disguise themselves as the film's superheroes so they can disable the warhead. Meanwhile, Megan undergoes a deep brain stimulation procedure and asks Sylvester not to tell Walter, causing Sly to work from the garage and have to sit out from partaking in his favorite comic book characters during the mission. Also, in order to forget about his affections for Happy, Toby's boxing improves and, with Cabe's help, he wants to fight in an amateur match.

6. Tech, Drugs, and Rock 'n Roll

The team is ready to open the new smart building project they have been working on with Elia, but the building has been infected by a swiftly spreading worm that was uploaded onto Walter's computer by a mysterious woman he met at a tech conference mixer the night before. It is turning the now dangerous building into a burning death trap for all inside, including three children, one of whom is the head of security's son. They must work to simultaneously stop the fire and find the person responsible for planting the deadly virus.

7. Crazy Train

With Paige and Ralph stuck on an out of control L.A. Metro subway train, the team must stop it before it derails. They discover that the runaway train's been sabotaged to clear the tracks for a heist to steal a $50 million collection of British gold coins. Walter, with sheer disregard to his personal safety, bravely jumps onto the 90 mph speeding train and successfully stops it from derailing. Paige gets scared of seeing this and due her insecurity of losing Walter, hits him. Later she apologizes to him for her juvenile behavior. Elsewhere, Toby has his first fight and gets knocked out in the boxing ring. Meanwhile, Happy seeks her own distraction from their failed relationship by going out with Chet, who is actually her comedy coach. The men then track her down at a comedy club where she totally bombs her science-based routine that only Sylvester appreciates.

8. Area 51

A CIA agent bribes the team to search for their top-secret flagship 27B/6 plane from the CIA's new Integrity Airlines after two agents go rogue and end up in Area 51 during a routine mission. Happy creates a gamma ray spectrometer to use in the base's "cone of silence". Toby makes predictions for the future by writing down what will happen on their case in sealed envelopes that usually turn out to be correct. Happy, Toby, and Sylvester donate their portion of the $350,000 CIA money to Walter for his research funding goals towards Megan's MS. Walter plans to upload Megan's consciousness into a hard drive as a technological singularity, Transcendence -style. Later, tension grows between Walter and Sylvester when Sylvester obeys Megan's wishes and does not go forward with the aggressive treatment of intubation that Walter wants.

9. US vs. UN vs. UK

The team works with MI6 to infiltrate the United Nations headquarters in New York City to stop Jonas Madaky, an ambassador/gun runner from the African nation of Buritan, from making a deal to supply militants with weapons to destroy their rebellious revolutionaries. However, things take a bad turn when the British operative turns on the team and blackmails Scorpion into helping assassinate Madaky. It appears that MI6 agent Gleason is killed and that the team decides to carry out the plan to take out Madaky. It is later revealed that Gleason is alive and Scorpion played a Houdini stunt.

They orchestrate Madaky's arrest and reveal that MI6 director Olivia Cromwell was in business with Madaky, leading to her arrest, as well. On the home front, Walter gets a court order to have Megan intubated, much to Sylvester's dismay. In order to protect Megan's wishes, Sylvester makes a bold decision and gets Ray, an ordained minister of the Immaculate Church of the Internet, to marry them, making Walter accept that the situation is beyond his control.

10. Arrivals and Departures

When Walter's parents visit Megan as her condition worsens, the hospital is infected by a fatal fungus outbreak cutting Walter off from his sister and placing the whole team at risk. Thinking it is stachybotrys, the infectious disease unit searching for a cure collapse by spraying the wrong fungicide. It now falls to Scorpion to search for a cure themselves. Toby examines gold dust, a natural fungicide, on a cafeteria worker's boots and sees the man cut his leg, becoming a host to Meliola anfracta, an ancient fungus unearthed in soil.

In a surprising discovery, Sylvester's OCD about using antibacterials has caused him to grow a superbacteria on his hands that is fatal to the fungus. With help from Ralph and Cabe, who the CDC keep outside, they spread the bacteria through the water standpipes and save those trapped inside. Walter reaches Megan in time to be at her side as she dies. Later, he receives an email with a video from Megan telling him that, he is more than just his brain, he is his heart and he should not be afraid to love. As a result, Walter begins to open up to his estranged parents and holds hands with Paige while sharing memories of his beloved sister.

11. The Old College Try

As the team deals with Megan's death six weeks later, they must stop a cyber terrorist, using code written by college students, who is threatening to shut down the Federal Reserve if they do not receive a quarter of a billion bitcoin in the next 72 hours. For their mission, they have to go undercover at a local university; Happy goes as a sorority pledge, Walter as a visiting drama instructor, Sylvester as a wrestling transfer student, Cabe as a campus security guard, and Toby a professor applying for a position in the Psychology Department headed by a former rival who stole his fiancée.

But, in order to foil this unknown hacker, they must get into the school's server, which is a highly sophisticated quantum computer, to kill the ransomware. Meanwhile, Walter conducts an experiment to prove that Ray's firefighting partner's death was not Ray's fault by using Tuggle's tank that Cabe's friend acquired from police evidence storage. Later, Ray discovers the submerged tank in liquid glycerin which would harden any air leakage from the tank to create a bubble pattern. The test proves the tank was defective, giving Ray the peace of mind to go back into the world again, leaving Scorpion headquarters.

12. Dam Breakthrough

On Christmas Eve, Scorpion receives a mission from the DWP at the Augustine Power Station on Mount Baldy, which may go critical after a 50-foot pine tree uproots and crushes the building's wall. If the transformer gets flooded and shorts, 100,000 people will lose power on Christmas Day. After they re-boot the computer and engineer the roof, they notice a mudslide spilling into the reservoir has put a crack in the nearby dam's wall following torrential rains. Now, they have to stop the dam from breaking and wiping out the town down in the valley by repairing it.

Walter deals with Megan's death by putting her ashes in a coffee can in his glove compartment and talking to himself. When Walter misplaces his pet ferret, he is so overwhelmed by the loss that his emotions finally get the best of him in front everyone; he really misses Megan. The Karmen Prize committee notifies him that he has won the $15 million grant, but he decides to launch the rocket to honor his sister.

13. White Out

Scorpion has to survive subzero temperatures trekking to the remote McMurdo Station in Antarctica to save a U.S. Special Forces unit in Darfur that is trying to take down a genocidal warlord eviscerating border-town farming villages. The Pentagon lost contact with a low geosynchronous orbit satellite that controls a military drone used to support their operation and the team needs to reconnect it to give cover to the four-man strike team. During the mission, Toby risks his life to save Happy after she gets cut off from the rest of the team by getting lost in a whiteout blizzard.

For her New Year's resolution, Happy starts reading Toby's rival Quincy Berkstead's book, Your Essential Strategies for Saying Yes to Life to be a little more positive and a little less mean and sarcastic, while Walter tries to be more social and Cabe gives up coffee to lower his blood pressure.

14. Sun of a Gun

Sylvester's estranged father Ken, a retired army colonel ( Jeff Fahey ), enlists Scorpion's help after discovering that the mythical Sun Gun, a deadly weapon of mass destruction, is actually real and was found in an old German bunker from World War II by an African president/dictator. The team goes to a North African nation to find out if the dictator has hidden metallic sodium panels that are capable of concentrating sunlight to be launched as a satellite death ray. During the mission, Walter must use dishonesty and flattery to get up close and personal with the megalomaniacal dictator, who is smitten by his intellect. Also, in order to be more social in their daily lives, Walter and Cabe decide to go speed dating together, but they are unsuccessful.

15. Da Bomb

The team is tasked with helping NASA find whatever alerted a possible system failure on their top-secret JC-49 rocket that is set to launch from an Air Force base. To their surprise, former Homeland Security director Merrick, who is now working for NASA, asked for Scorpion personally and begrudgingly works with them. However, the mission is threatened when Walter's date from the previous night, Linda, walks into the garage, handing him a jump drive with a recording of a scrambled voice giving them instructions to sabotage the launch or face the consequences of the bomb strapped to her chest. Meanwhile, Sylvester decides to audition for Jeopardy! in order to win enough money to buy the naming rights for the new pediatric wing at Megan's hospital so that it can be named after her, but he is nervous to be in front of the cameras.

16. Fractured

While Sylvester takes Ralph on an educational field trip to the beach, Paige forces Toby and Walter, who have been constantly fighting lately, into a couples therapy session specialized for business partners, but their therapist's ( Penn Jillette ) credentials are from online colleges and his methods are unorthodox. Cabe and Paige help to prepare Happy for a presentation of her newly designed airbag to a prospective client. Suddenly, a major 7.8-magnitude earthquake hits the L.A. area, causing significant infrastructure damage to the city including water main explosions and major fires. The team must work fast with limited resources to stop a broken gas main under Koreatown from exploding.

17. Adaptation

When Mexican drug runners start to use armed drones to smuggle extremely pure bricks of heroin across the border, Scorpion is tasked by the Policía Federal Ministerial to find a way to stop them. Walter and Toby continue their therapy and Dr. Rizzuto makes them use sock puppets to express their feelings. After being rejected by Jeopardy, Sylvester memorizes product pricing in order to be on The Price Is Right. Meanwhile, Toby and Happy's private relationship becomes public, leading Walter to issue them an ultimatum based on his rule against intra-team fraternization; either they break up or one of them leaves the team.

18. The Fast and the Nerdiest

An old ex-con childhood friend of Cabe's, Mick Doherty ( Eric Roberts ), approaches the team, asking for their help in stopping a group from smuggling a biological weapon into Balio in Central America. The team manages to infiltrate the garage of a high-end vehicle import/export business and, on Toby's bet, Walter is forced to challenge one of the mechanics to a drag race in order to stall for time while Happy searches the office for incriminating paperwork. Meanwhile, Happy and Toby have begun to fight regarding Toby's increasingly frequent gambling habit, and CBS suspects Sylvester of cheating after having won $100,000 on The Price is Right in memory of Megan.

19. Ticker

When Walter gets into a fender bender, he goes to the hospital and meets a nice little girl named Olivia who is in need of a heart transplant. However, Toby notices a patient with symptoms of the Nibori virus, a lethal disease found only in the Far East, and discovers the blood supply at Los Angeles' blood bank has been hacked, resulting in all the bags being mislabeled. Scorpion decides to help find the perpetrator in order to save Olivia's life, but they only have 4 hours until her surgery and need to find a sample of Lutheran AB negative, her incredibly rare blood type.

Back at the garage, the team competes in the "ScorpiOlympics," their version of the Olympic Games that is only for geniuses testing their mental and physical abilities. Also, Sly's prize-winning days are over when he receives rejection letters from multiple game shows after winning big on The Price Is Right.

20. Djibouti Call

Scorpion is hired by the F.B.I. to install a newly developed audio surveillance system on the only U.S. military base located in Djibouti, Africa so that they can pick up on terrorist chatter. But this is just a ruse in order for Cabe and his Homeland Security trainee, Tim Armstrong ( Scott Porter ), to run a top secret op across the border in Makuria, gathering intel on a businessman who raids antiquities from Middle Eastern museums and sells them on the black market to fund training, fake visas, and advanced explosives for terrorists. However, it turns into a rescue mission when the team must save Cabe after he is captured behind enemy lines. Also, Sylvester hires a lawyer named Haywood "Jahelpme" Morris ( Horatio Sanz ) from a TV commercial to help him get past the boilerplate contracts for game show auditions.

21. Twist and Shout

When a construction company that is clearing a site for a factory build unearths an ammunition belt belonging to a Marine patrol that went missing in 1971 near Pleiku, Vietnam, retired Marine John Pandova ( Josh Randall ) of the Defense POW/MIA Accounting Agency hires Scorpion to enhance his ground imaging technology and ground penetrating radar equipment in only two days to give him proof that the remains (including his father's) are still there. However, they only have two hours when they find themselves in the path of an F4 tornado. Later, after he receives a failing grade for his coding project, Ralph's college professor steals his sound wave software, causing him to hire Haywood as his attorney.

Tim asks Walter to a meal, but is rejected as Walter is going to call Linda, who came back, to set up a date, so he takes Walter's advice on having dinner with a smart, kind, beautiful woman and asks to meet up with Paige at the diner. Linda does not return his call and it leaves Walter by himself, trying to beat Tim's high score on Proton Arnold.

22. Hard Knox

In order to test their security system, Scorpion is hired by an agent from the Department of Defense to break into Fort Knox and steal a 300-year-old Prussian scepter, proving that their depository is not run properly by a private firm. However, they discover half a pound of polonium, a toxic substance, hidden inside the artifact and must escape the buildings' traps with it intact. Elsewhere, Haywood wins his first case by helping gain more time while Ralph proves in court that the software he created was actually his by bookmarking his code data with important dates, like when he first met Walter. Also, Toby has suspicions about Linda, who he believes is less attracted to Walter than suffering from damsel syndrome, experiencing the same endorphin / dopamine rush from when he saved her. Walter breaks up with her, pledging to remain friends, while Paige accepts a date with Tim.

23. Chernobyl Intentions

Scorpion is tasked with helping Oksana Nastrova ( Kathleen Munroe ) of the Global Nuclear Energy Council move an improved concrete sarcophagus in place over the old deteriorating sarcophagus at the Chernobyl Nuclear Power Plant before corium trapped under the reactor destabilizes. Toby, who has diagnosed ex-Scorpion team member Mark Collins ( Joshua Leonard ) as insane, remains in Los Angeles for Collins' competency hearing. Scorpion discovers unmelted caesium rods near the corium using a robot designed by Happy. While Paige and Sylvester fly with Oksana in her plane over the sarcophagus, taking measurements, the robot is affected by the radiation and punctures the corium, resulting in the ejection of a radioactive cloud that disables the plane.

It crashes into the old dome, trapping the plane's occupants while the team tries to save them and stop the corium from reaching the caesium rods. After returning to the United States, Walter tries to ask Paige out to a jazz festival, but decides to give her his tickets so that she can take Tim instead. Meanwhile, Toby covertly meets his jeweler in a parking garage to pick up a bespoke hex nut engagement ring for Happy, only to be kidnapped by Mark.

24. Toby or Not Toby

Scorpion has to outsmart the mentally-unstable Mark Collins, who has kidnapped Toby and intends to torture and kill him unless he receives Walter's BBI ( brain–brain interface ) research. But, if his demands are met, he has the ability to advance the technology to where he can read peoples' minds. When they find where Mark's hideout is through ham radio frequencies, Walter has to choose whether to capture his nemesis or let him go to disarm his elaborate booby trap—an intricate maze of dental floss holding a single jar of acid over Toby's head.

After Toby's brush with death, Walter catches up to Mark and captures him on a bus going to South Carolina, the location of his favorite childhood memory. Meanwhile, Sylvester lets Toby's marriage proposal to Happy out of the bag, but she has a marriage secret of her own. Later, Walter comes to his senses about Paige, realizing he loves her. He leaves to stop her from spending the weekend with Tim at a jazz festival in Lake Tahoe.