With crime in Starling City at an all-time low, Oliver thinks he can finally balance being both the Arrow and Oliver Queen and asks Felicity out on a date. Diggle becomes a father, Lance is promoted to Captain, Laurel joins Arrow's inner circle and Felicity gets a part-time job at a tech store to make ends meet. Oliver fights to regain his company, Queen Consolidated, but comes up against a very worthy opponent - the charming Ray Palmer.
Lance calls the Arrow when another archer appears in town and starts skewering businessmen. Diggle uses A.R.G.U.S. to find the archer's identity; he is a man named Simon Lacroix, who goes by the codename Komodo. However, the team hits a rough patch with the mission and gets help from a surprising source - Laurel. Meanwhile, Oliver begins to worry that he hasn't heard from Thea, which forces Roy to tell him the truth about why she left town. Ray Palmer pursues Felicity. In the flashback, Maseo tells Oliver that Amanda Waller has ordered his first kill. As Oliver looks down the scope of the rifle, he sees the target is his best friend, Tommy. Despite her promise to her sister, Laurel debates sharing a secret about Sara with Lance.
Oliver decides it's time for Thea to come back to Starling City, so he packs for Corto Maltese, where Felicity has traced Thea's whereabouts. Lyla asks Diggle to go with Oliver because one of her field operatives, Mark Shaw, has gone dark in Corto Maltese and she'd like him to look into it. Feeling responsible for Thea's departure, Roy joins Oliver and Diggle on their journey. Shaw double-crosses Diggle, putting numerous A.R.G.U.S. agents, including Lyla, at risk. Meanwhile, Laurel meets Ted Grant, and Felicity adjusts to her new job.
Nyssa believes that Malcolm killed Sara and goes after him to avenger her lover's murder. Oliver discovers that he has no choice but to stop her, despite Laurel insisting that he avenger her sister's death. Meanwhile, Thea returns to Starling City and settles in... until Nyssa discovers that she's Malcolm's daughter.
When a cyber attack brings Starling City to its knees, Oliver and Felicity are pushed to their limits to contain the destruction. Life gets even more complicated for Felicity when her mother, Donna, stops by for a surprise visit. Ted questions Laurel's motives. Thea buys an apartment with Malcolm's 'estate' money.
After a body is found strung up in the Wildcat gym, Ted becomes the main suspect. Oliver and Laurel argue over Ted's innocence. When Maseo needs Oliver to remember where an informant for China White stashed key information, he asks Tatsu to help jog Oliver's memory. Roy shares a secret with Felicity.
Oliver must stop an Arrow-obsessed serial killer, Carrie Cutter, who is convinced that The Arrow is her one true love and will stop at nothing to get his attention. Unfortunately, her way of getting his attention is to kill people. Meanwhile, Ray asks Felicity to be his date for a work dinner with important clients. Thea auditions new DJs for Verdant and meets Chase, a brash DJ with whom she immediately clashes.
As Barry, Caitlin, and Cisco arrive in Starling City to help with the investigation into Sara's murder, former Suicide Squad member Digger Harkness goes after Lyla. The Arrow and his team need all the help that they can get to stop the boomerang-wielding killer, particularly when he sets five bombs in the city to cover his escape. In the past, Amanda Waller teaches Oliver how to make the hard choices... whether he wants to or not.
Nyssa returns to Starling City and tells Oliver that her father, Ra's al Ghul has given Oliver 48 hours to find Sara's killer or the League of Assassins will start killing the citizens of Starling City. Laurel is stunned when her father delivers a very special Christmas gift - her mother, Dinah. Meanwhile, Ray tries to make amends with Felicity and Oliver sets a meeting with Ra's al Ghul.
In the aftermath of Oliver's fight with Ra's al Ghul, Diggle and Arsenal continue to protect the city in the Arrow's absence. However, after three days without hearing from Oliver, they begin to fear the worst may have happened to their friend. Felicity refuses to believe that Oliver could be dead until Merlyn pays the team a surprise visit. Thea suspects there is something more behind Oliver's disappearance and asks Merlyn for a favor. Meanwhile, Ray tests a part of his new suit and Laurel takes up the mantle of the Black Canary.
Arsenal and Diggle confront Laurel about trying to step into her sister's shoes and warn her to stop before she gets herself killed. However, when Brick kidnaps the city's Aldermen and threatens to kill them all unless the police evacuate The Glades, it's all suits on deck. Meanwhile, Ray steps in to help Lance and the police force fight Brick, showing Felicity a new side of her boss. Malcom tells Thea that Ra's al Ghul is after him and his family and they must leave town immediately.
Still operating without Oliver and desperate to stop Brick, Team Arrow is forced to consider Malcolm's offer to help shut Brick down as Malcolm has a personal score to settle with the felon. Roy and Laurel point out that the team could use some help to save the innocents of The Glades, but Felicity is adamantly against it. They look to Diggle to make the final decision. Meanwhile, the flashbacks chronicle Malcolm's descent from kind-hearted father and husband to cold-blooded killer after the murder of his wife.
Oliver is thrown by the changes within Team Arrow. He's used to calling the shots but sees that the team has evolved in his absence and tensions quickly escalate in the lair. Oliver is furious that Laurel has been going out as the Black Canary and tells her to stop risking her life, but when Vertigo hits the streets again, Laurel goes against Oliver's wishes and tracks down Vertigo who hits her with a full dose of the drug. Laurel's biggest fears revolve around her sister Sara so the Vertigo causes her to hallucinate an epic fight between Canary and Black Canary. Meanwhile, Chase surprises Thea, and Roy warns Thea to stay away from Malcolm.
Malcolm puts Oliver and Thea in a dangerous situation that lands them on Lian Yu with Oliver's former enemy, Deathstroke. A flashback reveals when Oliver and Maseo returned to Starling City to retrieve the Omega bio weapon, and despite being under strict orders from Amanda Waller not to reveal himself to anyone, Oliver looks in on his family, Laurel and Tommy.
Malcolm is captured by Ra's al Ghul and taken to Nanda Parbat. Because of his love for Thea, Oliver considers saving Merlyn. Ray is obsessed with finishing his Atom suit so he can save the city but Felicity fears he is heading down the same path as Oliver and tries to pull him out of the lab.
Still weighed down by his last meeting with Ra's al Ghul, Oliver returns home to find a new villain and his crew has started terrorizing Starling City - Michael Amar AKA Murmur a man whose mouth has been sewn shut. Meanwhile, Laurel and Nyssa bond over their issues with their fathers and Nyssa makes Laurel an offer. Thea is forced to come to terms with her father after Oliver brings Malcom to the loft to recover, and Lance shuts out both Laurel and the Arrow.
It's celebration time as Diggle and Lyla get married. However, Deadshot interrupts their honeymoon, and tells them the Suicide Squad has been given a new mission - rescue United States Senator Joseph Cray from a hostage situation in the Republic of Kasnia. Amanda Waller breaks down the mission and introduces them to the newest member of the Suicide Squad, Cupid. Meanwhile, Oliver learns about Ray's new Atom costume and the two have a heated stand-off. Felicity and Ray hit a rough patch.
During an attack on the mayor's office, Ray is critically injured. Felicity is pleasantly surprised when her mother, Donna Smoak, shows up at the hospital to offer her support. With the SCPD out in full force looking for the assailant, Oliver and his team work hard to stay one step ahead of the police to find the man responsible. However, things come to a head when Ra's al Ghul kidnaps Captain Lance.
Lance continues his mission to take down the Arrow so Felicity orders Oliver to keep a low profile. However, when a meta-human named Jake Simmons, who kills people with blasts of energy and plasma, starts terrorizing Starling City, Oliver is forced to ask Ray for help. The unlikely duo is forced to team up to save the city.
Ra's al Ghul finally makes Oliver an offer he can't refuse. The team joins Oliver on his journey to Nanda Parbat where a heartbroken Felicity decides to take matters into her own hands.
Oliver goes through a rigorous transformation. The League of Assassins sets their sights on Nyssa, who is back in Starling City training Laurel. When Nyssa realizes they are coming, she arms up to face them alone but Laurel asks Felicity and Diggle to help protect her new friend.
Ra's tells Nyssa that she must marry Oliver or face death. Meanwhile, an unexpected ally travels to Starling City to ask Diggle, Felicity, and Laurel to help infiltrate Nanda Parbat. In the past, Maseo and Oliver try to find the cure for Akio before it's too late.
Everyone's lives are in danger as Ra's al Ghul puts forth his final plan. Oliver/Al Sah-him must decide if he's strong enough to take on this new role and what it will mean for everyone on Team Arrow, and his soul.