In February 2011, Theo realizes Shawn has betrayed him and decides Shawn has to be taken out so after Jason and Shawn attempt to lure Theo to a location he sends his men in his place and orders them to open fire turning it into a shootout. Jason got away but Carly finds a wounded Shawn passed out on the side of the road and brings him to her house and helps him by tending to his wound. Sonny Corinthos, Carly's ex soon arrives at her house looking for Shawn as he blames him for having a role in planting the car bomb that led to the disappearance of his now-wife Brenda. Shawn tells Sonny he had nothing to do with it and that it was all Theo's plan. Sonny doesn't believe it and has his goons tie Shawn up with orders to kill him if he doesn't talk. Sonny ultimately doesn't do anything and when he leaves, Shawn is taken to the hospital to get proper care.
When serial killer, Franco begins menacing Carly and her daughter Josslyn, Jason hires Shawn as their personal bodyguard. Jasper Jacks, Carly's estranged husband strongly objects to Shawn guarding his daughter as he doesn't want someone with ties to the mob protecting Josslyn. He attempts to pay Shawn to quit but Shawn states that he can't be paid off.
Jax then digs into Shawn's past and finds out he had been dishonorably discharged from the military because he had killed a fellow Marine. Jax then threatened to use Shawn's violent past against Carly during their custody hearing to prove Carly's an unfit mother. Carly defends Shawn but he quits, not wanting to have anything to do with messing up Carly's chances at keeping her daughter. Shawn then confronts Jax by telling him he quit. Shawn ordered Jax to leave Carly out of whatever issue Jax had with him. Jax then taunted Shawn about killing another Marine and Shawn responds by punching Jax in the face.
In July 2011, Jax lost custody of his daughter to Carly after Sonny framed him for drug possession and Jax quickly leaves town. Shawn believes Jax will be back and begins paying more attention to Carly and her daughter. In August 2011, Shawn's instincts were right and Jax comes home attempting to kidnap Josslyn. Shawn catches Jax before he's able to leave but his efforts are stalled when Jax brings up an incident in Shawn's past where he unintentionally injured a young girl during the same event that caused his PTSD.
Shawn started to remember the incident and he froze and Jax walked right out the door with Josslyn. Shawn recovers and he starts going around town looking for Josslyn. He manages to track Josslyn and Jax down at Robin Scorpio's house. Shawn talks to Jax who eventually gives Josslyn to Shawn and Shawn brings her back home to Carly.
When Jax is presumed dead after his private jet crashed into the harbor, Shawn comforts Carly but a body wasn't found making her believe Jax is still alive. Shawn encouraged her to trust her instincts and gave her more hope when he found out Carly's boat was missing from the harbor. Jason later approaches Shawn with a job to take over his position in the Corinthos Organization temporarily while he is preparing to marry Sam. Carly and Shawn continue to grow closer as he becomes more involved in the business. He protects Carly’s son Michael from getting busted with illegal drugs that were planted in Sonny's warehouse. However, Michael doesn’t approve of his mother’s and Shawn’s budding relationship.
On September 30, Shawn and Carly are accidentally locked in a panic room in Sonny’s warehouse as Shawn was preparing to put seven bags of hydrocodone in the room. Sonny’s rivals had planted the bags for the cops to find and Shawn had arranged for a fake bomb to be found in the warehouse to keep the cops busy.
In October 2011, after receiving a package from Franco, Carly becomes worried and she and Shawn go to Hawaii to warn Jason, who is on his honeymoon with new wife Sam. They stay with Sam and Jason and bond and ultimately share a kiss on October 27.
In November 2011, on Veteran’s Day, Shawn opens up to Carly about his friend and fellow Marine Tommy Ashford whom he accidentally killed in Afghanistan and how his father was gunned down right in front of him when he was a kid. Carly and Shawn spend Thanksgiving together at Kelly’s but Shawn realizes they are getting too personal and pulls away. When Franco makes contact again, Shawn moves in with Carly temporarily to protect her and Josslyn.
In December 2011, Shawn and Jason's accountant Bernie Abrahms attended a meeting in Jason's place but it was an ambush and Bernie is shot by an unknown assailant. Shawn handled the situation but he was overcome by his PTSD. Carly arrived soon after and was concerned over the state of shock she found Shawn in. Carly soon found out that therapy dogs can help with PTSD and for Christmas, she gets Shawn a dog to help with his PTSD, whom he names Wilson.
On December 28, Shawn tells Carly he can’t take Wilson. Carly says he is giving her mixed signals and he kisses her before saying no. Carly says Franco is gone and she is moving to the Metro Court with Josslyn. She will keep Wilson and dismisses Shawn.
In January 2012, as Shawn is preparing to leave Port Charles, he is forced to take in Tommy’s troubled teenage son, T.J. Ashford who has run away from home. Shawn decides to take him in. Carly then hires Shawn to manage Kelly's Diner. Shawn is jealous of Carly's new relationship with Johnny Zacchara and T.J. calls him out on his feelings for her. On January 12, Carly meets Ranelle, a woman Shawn is seeing. Ranelle clarifies that she has no commitment to Shawn and they are casual. Carly explains that she and Shawn are just friends.
Shawn later tries to convince Carly to officially divorce Jax when Jax sells his half of their hotel to Carly's rival, Kate Howard without telling her. On February 2, 2012, Shawn asks Carly on a date. She is taken by surprise and says she thinks they are in a good place right now and he agrees.
At the urging of GH's new resident psychiatrist, Ewen Keenan, Shawn asks to escort Carly to the General Hospital Pulmonary benefit at the Metro Court, but she doesn't return his call. After much probing from T.J, on February 23, Shawn confronts Carly and tells her he wants to be with her. When she doesn't return his feelings, Shawn backs off.