At the end of the first season, Danny finds out that Rachel is pregnant with their child and is leaving with Grace to go back to New Jersey; Danny wants to come with them but is conflicted when McGarrett is in danger. As Season 2 begins, McGarrett is in jail awaiting trial and Danny comes to visit him with a special guest. Danny finds out that Rachel's intentions may be different than he was hoping for. The task force get a new team member whose job is to keep them in line. Chin Ho worries about Kono's safety and a new case targets the task force members and threatens their safety.
McGarrett is in prison awaiting trial for the murder of the Governor. Danny visits, bringing a surprise guest, McGarrett’s SEAL Lt. Commander Joe White (Terry O’Quinn). Shortly after they leave, Victor Hesse shivs McGarrett in the yard which sends him to the emergency room. McGarrett escapes from the ambulance and makes his way to Max’s house, who treats him and helps reunite McGarrett with his team (except Kono) who now are working together to exonerate McGarrett. Joe recognizes a medal from McGarrett’s father’s lock box and takes McGarrett to see and elderly Japanese man named Mokoto. Mokoto worked with McGarrett’s father to help clean up the HPD. He also gives additional intel that helps Jenna Kaye trace a key from the lockbox to a locker in the Molokai airport. Danny and McGarrett find a memory card with video footage from a camera McGarrett’s father set up in the Governor’s study. Our team realizes the hidden camera may still be there. They find the camera and there’s footage to exonerate McGarrett. The team gets reinstated. Kono has been suspended from HPD pending further investigation of the evidence forfeiture locker theft. Also, we learn that Danny’s ex-wife Rachel has gone back to Stan, turns out she figured out the baby was his and she wants to put their marriage back together.
The new Governor assigns a Homeland Security agent, Lori Weston to the Five-0 task force. As a profiler, she brings real skills to the job, but she’s also there to make sure McGarrett and the team abides by the new rules (no immunity). McGarrett gets called away from the meeting to go investigate the kidnapping of a 15 year old champion paddleboarder, Jen Hassley. Jen has a heart condition and lost her medication so time is of the essence in finding her. McGarrett tries to sideline Lori by having her babysit the family; however, she ends up finding a key clue to identifying Jen’s kidnapper – the identity of a man who has been emailing Jen about meeting her birth mother. Jen’s parents were told the birth mother was dead, and when they find the man’s apartment, it looks like he’s using personal information about a number of girls and could be a pedophile. They track down one potential victim and discover that their alleged pedophile is actually a cult extractor. Our team deduces that Jen is the granddaughter of a local cult leader and he’s kidnapped her. With Lori’s help, McGarrett rescues Jen. Chin Ho is worried about Kono; HPD IA Lt Fryer has been interrogating her and ultimately decides to have her kicked off the force. Jenna Kaye returns to Washington to follow up on a CIA lead that her fiancé may still be alive.
McGarrett’s friend and mentor Joe White asks McGarrett to investigate the death of SEAL team member, Max Garcia who apparently committed suicide. McGarrett persuades Max to redo the autopsy (Max’s boss did the original), and Max discovers that Garcia was murdered and now Five-0 (including Lori Wilson) can officially investigate. Joe helps the team by getting whatever information he can from the military and when a second SEAL from the same team is found murdered; McGarrett realizes they’re being targeted. They work to find the killer and the motive for these murders in order to save the rest of the team and McGarrett manages to rescue the final team member unaccounted for in a daring sky dive maneuver. Chin Ho worries when he learns that Kono is hanging out with a bunch of dirty ex-cops ever since she was kicked off the force.
Swimmers are disturbed when they find a floating hand in the water. The hand belongs to Blake Spencer, a deep-sea diver who is known for his shipwreck finds. When they find the rest of his body and it’s clear he was a murder victim. Closer inspection of Blake’s life reveals that he had invested everything into a mysterious big dive that seems to be connected to some Spanish Galleons they find in his apartment. When they learn from a local expert the coins are fake, their number one suspect is the businessman behind the dives, since he might have killed Blake to keep the secret that the shipwreck had been "salted”. Tracking the boat Blake used, our team finds that Blake’s secret project was a hearse that had fallen off a ship during WWII that was carrying cash that was supposed to have been destroyed in a crematorium and replaced with "Hawaii-overprint” currency. Blake’s secret dive was discovered and the two men who discover it double-cross him for the money. Ironically, Blake wasn’t interested in the money, he only cared about the casket in the hearse–it carried the body of his grandfather, and he wanted to give his dying mother her last wish to have it recovered. Also, Chin Ho learns that Kono used his ID to access police records. After enduring some teasing from McGarrett, Danny ends up asking out the coin expert.
The Five-0 team investigates the murder of Honolulu State’s Women’s Volleyball team Coach. The Coach lives in the guest house of one of the University’s wealthy patrons, and when they find compromising pictures of one the player’s on the team, McGarrett wonders if the Coach was killed because he was threatening the player. The player defends the Coach and said he was protecting her. Further investigation takes Chin Ho and Lori to a motel the Coach was renting. There they quickly discover Trisha, the wife of the Coach’s landlord has been staying there. They wait for her return, but give chase when a thug breaks into the room. They shoot the thug, but he escapes into a waiting car being driven by Kono. When the team brings in Kono, Captain Fryer shows up, furious at Five-0. Turns out, Kono’s suspension and bad behavior has all been set up as she’s been working undercover to infiltrate a group of former cops who are running illegal businesses. When Trisha left her husband, she emptied their bank accounts, not realizing he was money-laundering for the dirty cops. Unfortunately, the Coach got in the cops way when he tried to protect Trisha. Chin Ho reconnects with his former fiancée, Malia, and confesses his concern about Kono’s recent behavior but when Malia tries to talk to Kono, she shuts Malia down. Danny’s apartment is being torn down and he has to find a new place.
The apparent home invasion robbery/murder of a local celebrity chef connects to a series of home invasion robberies perpetrated by a group of valet parkers. As our Five-0 team investigates the valets, things don’t quite add up and they figure out the home invasion was staged to cover up the murder. Taking a closer look at the chef’s personal life, they discover he sponsored a local charity that trains kids to be MMA fighters to keep them off the streets. His sister now runs the charity organization and one of the fighters who works out at the gym has a past record of violence. When Five-0 find the murder weapon in his apartment, it seems like a closed case, but there’s one final twist in finding the killer. Because the main fighter was injured when McGarrett went after him, McGarrett ends up having to "pinch-hit” for the fighter in a charity MMA fight.
A young couple filming a spooky documentary about a traditional Hawaiian burial site are murdered in this Halloween episode. A homeless man who considers himself to be the protector of the site, curses Danny, and Danny seems to have a run of bad luck afterward. A fingerprint on one of their victim’s face gives Fvie-0 a solid lead, except that their putative killer is dead. Convinced he faked his own death, McGarrett and Lori interview the girlfriend who confessed she killed him. It’s a puzzling case with lots of conflicting leads, until they find body parts on multiple victims also buried at the site. The new victims all connect to the same mortuary where all the bodies (most dead from natural causes) were meant to be buried. Danny thinks he may have found the perfect new apartment and he negotiates a great price because a murder took place inside, however when he discovers it’s haunted he walks away from it.
A group of "tow surfers" remove a body from a plane that crashes into the ocean and it turns out to be a DEA agent. McGarrett and the team work with the victim's DEA boss and start investigating the drug cases she was working on. She was doing surveillance on local medicinal marijuana shop and had interviewed a number of their customers, but there doesn’t seem to be anything that leads to her murder. When they find the man who stole pages from her case journal, they’re able to restore the pages enough to get an address, only to discover she was investigating the secret world of exotic medicine. It’s a world that promises cures to cancer, but doesn’t always deliver and the killer killed her because he thought she was going to cut off his supply to his miracle drug. After her death, he realized the medicine wasn’t working and he kidnapped the healer who was supplying him and Five-0 has to find the healer before he dies too.
After a police chase through a shipyard, police grab the high-end car thieves, but get an unexpected surprise. A dead body in the trunk of one of the stolen cars, with his face wrapped up like a mummy. The victim’s fingerprints have been sanded down and he’s clearly had plastic surgery to change his appearance, but Max helps them with their first lead, by identifying the doctor who put in the facial implants. McGarrett and Danny talk to the doctor, but he’s not helpful: the man used a fake ID, refused to have his pictures taken and paid in cash. Meanwhile, the rest of the team pursues the car thief ring, hoping to possibly find the killer. Finally, a hotel key in the car leads our team to the victim’s girlfriend who reveals he’d been working on an oil rig when something happened and he said they needed to disappear. Turns out, the victim had left witness protection and disappeared when his cover had been blown. Someone from his old neighborhood recognized him and called the mob boss who wanted him dead. But in a surprise ending, the mob hit men hadn’t killed him. Also, Danny, still searching for an apartment has been sleeping on McGarrett’s couch. It’s an arrangement that suits neither of them.
An investigative reporter is murdered and Five-0 believes her death may be connected to her work. Meanwhile, Jenna Kaye asks McGarrett for his help delivering a ransom to rescue her fiancé who is being held by rebels in North Korea. McGarrett agrees and the mission goes south fast: Wo Fat used Jenna to set a trap for McGarrett in order to find out what he knows about "Shelbourne". Meanwhile, Danny and the team figure out that the reporter's death is connected to Jenna and when they lose contact with McGarrett, they enlist Joe White's help to rescue him. Without sanctioning from the military, Joe puts together some men to join Five-0 and they head to N. Korea to rescue McGarrett.
A busload of school children is kidnapped and McGarrett and the team are puzzled by the ransom demand: the kidnappers want the $80 million worth of cocaine Five-0 recently seized. As the team works to locate the missing children, Danny and McGarrett question Vargas, a low-level courier and the only man who survived the recent drug bust. He doesn’t seem to know anything but Kono works with him and gets him to retrace the route they took. They manage to locate the warehouse and though it contains the missing bus, the children are gone. McGarrett manages to get the Governor to let them use the confiscated drugs as bait, but when they put the drugs in the drop car, the car is immediately blown up. With the evidence destroyed, Vargas will go free, and the team realizes that the kidnappers went to a lot of trouble to free him, meaning he’s much higher up in the cartel than he’s admitted. With time to find the children running out, McGarrett and the team put together a bunch of other leads in order to locate them and manage a daring rescue in a rock quarry.
Exploring an abandoned WWII bunker, three teenagers discover a body and our 5-0 team is called in to investigate. Upon arriving at the scene, they quickly find out the victim is still alive. Following several leads, McGarrett and the team stumble onto an investigation led by Fryer, who is looking into the murder of a Jane Doe. Ultimately, they discover the victim was searching for his missing son; Fryer’s Jane Doe and the proprietor of a tourist bar were working to scam the distraught father out of the reward money he offered to find his son. The 5-0 team is able to find the son's real killer and get a confession out of him.
Adam Noshimuri, Hiro’s son, confronts McGarrett about his missing father and Chin Ho and Malia get married.
Five-0 investigates the death of a teenage girl, found murdered in her bed. After pursuing a number of leads related to her friends and family, they discover that the murder was filmed by a student who had been using laptops to secretly record people. Though the face of the killer was obscured, it’s clear that the murder was a professional hit and finding out why this girl was targeted is the key to finding her killer. The only thing unusual about the girl’s life is that her father is serving on a jury for a small construction-related civil lawsuit. McGarrett and the team figure out the case has far-reaching ramifications and replacing the father on the jury by killing his daughter, was the key to squelching the case.
McGarrett and the team get called in when a delivery truck is hijacked. Initially, it appears as though nothing is missing, however, our team quickly figures out that the driver was picking up items from the airport, bypassing regular security, and dropping them off in between stops. Unfortunately, this particular shipment was stolen before it was dropped off. McGarrett then enlists help from Sang Min, who’s been solitary confinement, to help him gain access to one of the top smugglers on the island. When they finally get to the smuggler, they learn that the order was for chips used in passport-making. The customer was a regular of his. The customer had placed a large order and though the smuggler now can’t make delivery, he’s not complaining. This leads McGarrett to believe the customer was the one who hijacked the shipment. The team heads to a shop owned by Richard Detweiller; Detweiller had made a hundred passports for two eastern Europeans. They hijacked the shipment and shot Detweiller when he finished, but the team catches up with them at the airport.
McGarrett and his team launch a manhunt for two passengers who escaped through the wheel-well of a plane shortly after it landed. The plane was on lock-down because a US Marshall was murdered just as the plane started its descent. The Marshall was a friend of Danny’s from New Jersey and it turns out he was calling Danny when he was murdered. The team quickly finds the first escapee, he was the Marshall’s prisoner and he claims not to know the man who helped him escape. While Five-0 tries to find the second escaped passenger (known to them by his fake ID, McGuire), Danny gets a call from him. Turns out "McGuire” is Danny’s former partner, whom Danny put in jail. He’s out to ruin Danny’s life and has kidnapped Grace. Unable to contact Five-0, Danny must follow his ex-partner’s instructions in order to rescue Grace.
A Jane Doe is murdered at a hotel that's playing host to three separate large events, including a black-tie fundraiser hosted by Governor Denning that the Five-0 team attends. While Danny and Chin Ho investigate the crime scene, Lori and Kono follow a lead and learn the name of the murder victim, Vicky Chase. McGarrett and Kono interrogate Vicky's sister, Amanda, who begrudgingly admits that she was raped by an executive who attended the Governor's fundraiser, Dmitri Kirov, and that's who Five-0 thinks killed Vicky. The team learns that Dmitri is a Russian citizen and eventually determine that the Russian Consul General is hiding him in the Russian consulate. In order to lure Dmitri out, Chin Ho drives a van full of hazardous chemicals through the gate of the consulate and arrested by Russian guards before he can get out. Still, the plan works; the consulate is evacuated and McGarrett locates Dmitri and gives chase on foot. Just before Dmitri can make it safely back to Russian soil, both he and McGarrett are blindsided by a car and end up in the hospital. Kono swipes some of Dmitri's blood and gets it to Max, who runs tests and determines that Dmitri was indeed Vicky's killer. The Governor then bargains with the Russian Consul General and secures Chin Ho's release, but the backlash from the incident forces Lori to resign from Five-O. McGarrett and Catherine were originally planning on spending the weekend together for Valentine's Day since she was on leave from her ship, but the case prevents that from happening. After the team nabs Dmitri, McGarrett informs her that he's taking a few days to do some reserve training on her ship, just so he can spend time with her.
When a man dressed as a Hawaiian NaKoa warrior is found murdered in the jungle near the site of a large historical reenactment, Five-0 is tasked with tracking down his killer. The warrior is actually Brandon Koruba, a wealthy businessman who owns a boat company with the rights to build an inter-island ferry. The ferry poses a threat to local wildlife, so Brandon and his company have been beseiged with threats from radical environmentalists, but the none of the threats were legitmate. Eventually, Five-0 discovers a phone call that Brandon received just before he was killed, which leads them to Tony Schmitt, Brandon's business partner. Brandon had caved to the pressure from the environmentalists, but Tony didn't want to lose the money they would make from the ferry, so he killed his partner. Meanwhile, Danny struggles to find an appropriate time for Gabby to meet Grace. Danny finally arranges for them to meet and play at the beach while the Five-0 team has drinks next door, and Gabby and Grace hit it off immediately.
When a famous radio DJ is killed by an explosion in his yacht studio, Five-0 joins the case to hunt for the person who planted the bomb. Evidence initially leads McGarrett and Danny to Tony Archer, an ex-NYPD bomb technician living on a dilapidated houseboat. Tony turns out to be the godfather to Melissa Bates, the dead DJ's daughter, and he wants to find out who murdered his friend. He teams up with Five-0 to track the murderer down. Eventually, the team discovers that Melissa's husband, Todd Hegman, was part of a wanted con artist team that planned to steal money from the family trust. Todd fell in love with Melissa and didn't want to go through with the plan, so his partner, Karen Rafferty, killed Melissa's father in hopes that Todd would pay her off with the inheritance money. Also, Danny starts to fret over the level of attention Grace is getting from one of the boys in her class.
McGarrett's sister, Mary, is arrested by TSA agents for trying to smuggle $20 million worth of conflict diamonds on a flight, but McGarrett doesn't believe his sister is guilty of the crime. Mary insists that she was forced to commit the crime by an unknown man, who threatened to kill her coworker Angela. Five-0 then plans to put the diamonds on a direct flight to New York to save Angela, but the police officers escorting the diamonds are killed and the diamonds are stolen. With help from Chief Fryer, Five-0 tracks down August Marsh, an ex-con who served 30 years in prison for smuggling; if someone wants to move $20 million in diamonds, he's sure to know about it. March helps the team stage a sting, where they learn that the mastermind of the diamond heist was Kaleo, whom they put away in episode 107. Eventually, Five-0 figures out that Angela had been working for Liberian diamond smugglers for a while, and that she decided to steal the diamonds for herself. This is enough evidence to clear Mary of charges, despite Angela still being on the lam. Unbeknownst to the team, Angela arranges to sell the diamonds to March, who promptly kills her and takes the diamonds for himself.
Five-0 is called to investigate the murder of a young woman found in a drainage ditch on the North Shore. Max is convinced that a serial killer called the Trashman is responsible, but a man named Richard Nettles was sentenced to life in prison for the murders years ago. Max then informs the team that his biological mother was one of the Trashman's victims, and that he has been in contact with Nettles, who he believes is innocent. McGarrett and Chin Ho speak with a retired HPD officer who corroborates Max's beliefs, stating that he was never certain Nettles was responsible for the murders. Five-0 then sets out to find the connection between all the victims, and they discover that all of the women who were murdered had abandoned their children at Saint Mary's Church. McGarrett and Danny find incriminating evidence that ties the groundskeeper to the murders, but his alibi checks out. Max ventures over to Saint Mary's alone to investigate, only to be taken captive by the real Trashman, Deacon McDonagh. Once the team figures out that the Deacon is their killer and that Max is missing, they race over to Saint Mary's to save him. Max manages to escape his bonds and stabs the Trashman, killing him. McGarrett tells Max that his mother would be proud of his actions. Meanwhile, Kamekona's shrimp truck goes missing and he enlists Five-0 to help him find it. Danny tracks it down and returns it to Kamekona, who, it turns out, had forgotten to renew his vendor's license for the truck.
Five-0 and the NCIS: Los Angeles task force team up in Hawaii when there's a suspect on the loose who is threatening to release a deadly virus into the population.
Just as McGarrett finally gets his hands on his arch nemesis Wo Fat in a special ops raid, he's blindsided when he finds that the Japanese Yakuza is hot on their trail and wants them both dead.
Five-0 is in hot pursuit of a shooter who guns down one of their own, while another team member is forced to choose which of their kidnapped loved ones will live.