In the category, the Rich have hard lives, this relationship had a creepy guilt and shame dynamic.
Boone Carlyle was Shannon's stepbrother. Before Flight 815, he had been used by Shannon for money and as a result of this, his love for her was revealed and they had a one-night stand.
Boone Carlyle was the son of Sabrina Carlyle, and stepson of Adam Rutherford, a man who was killed in the auto accident in which Jack "saved" Sarah. When Sabrina and Adam married when Boone was ten, and Shannon, who was two years his junior, became his step-sister. His parents frequently left him with a nanny when he was young, and Boone, angry at being left alone, called her to his room repeatedly without cause. During one of these calls, when Boone was six, the nanny fell and broke her neck. This may be the impetus of Boone's character trait of helping Shannon throughout her life; guilt.
By the time he had turned 20, Boone was living in New York. After flying back to Los Angeles for Adam Rutherford's funeral, Boone comforted Shanno by giving his underage stepsister some alcohol to mollify her grief. He told Shannon she could live with him in New York if it would help get her career as a dance instructor started. After Shannon got the job, Boone was then offered a job by his mother. He accepted the job as the Chief Operating Officer of the wedding clothing subsidiary and he had to move from New York. Shannon had asked him to ask his mother for some money, but he came back empty handed. He that said his mother knew why he asked for the money. Boone then offered Shannon some of his own money to get her started in New York without him, but she refused because she wanted to prove herself. Shannon would fail in her attempts (feeble at best) to be self-sufficient and independent. She was daddy's little girl, who got anything she wanted from him, but when he was gone she was mad that her life had been so disrupted by his death. She would be seeking out other men to take care of her. She polished a devious streak to get what she wanted from men.
Although he would not openly admit it to anyone, Boone was in love with Shannon and he would do anything to help her out of her jams. He paid men to end Shannon's abusive relationships. Shannon would take advantage of Boone's feelings. He received a phone call from Shannon pleading for him to come and help her with her boyfriend, Bryan, in Sydney. Boone flew to Australia and, although she initially denied there was anything wrong, Shannon showed him a bruise on her forehead discreetly, as Bryan kicked Boone out of their house. He went to the police station to file a report but the Detective was unwilling to help because Boone and Shannon were not blood related, and joked, they were not the "dating police." Boone decided to take matters into his own hands.
He tried to bribe Bryan to leave Shannon. He took the money, but when Boone came to pick up Shannon, Bryan was still there - - - willing to share the loot with Shannon. In other words, Boone was conned into giving Shannon $50,000. There was a fight, and Boone lost. Later that night, Shannon appeared at Boone's hotel room and told him that Byran had left her, taking all the money. They had drinks, and the alone Shannon seduced Boone. Afterward, Boone felt confused and dejected when Shannon suggested that they return to LA and act if nothing happened that night.
Throughout his time on the Island, Boone would spend a lot of his time with Shannon before finally getting over his love for her and letting her go. He later became Locke's apprentice when the two discovered the Hatch and they formed a close friendship. Unable to open the Hatch, they followed a dream Locke had and found a small plane sitting on a cliff. Boone climbed up into the plane but suffered severe injuries when the plane fell to the ground. Despite Jack's best attempts to save him, Boone realized he was going to die and told Jack to let him go. After Boone's death, Locke described him as a "sacrifice the Island demanded."
Shannon's time on the island was not one of personal growth. She kept to her spoiled trust fund persona, rarely helping out. Boone's death did affect her deeply, but it may have been slightly more shame on how she treated him that deep affection. For Shannon, being totally alone, began to seek out company of someone to support her. That person was Sayid, but their relationship was very brief, as Shannon was killed accidently by Ana Lucia. Sayid's grief over Shannon's death was much more than Shannon had when Boone perished.
So despite the close relationship between Boone and Shannon, they were not "together" in the after life reunion. For little apparent reason, Sayid was reunited with Shannon (and not Nadia). And Boone, like his friend Locke, had no one to sit next to during the final church sequence. Why Boone, who only tried to help his step sister throughout her life, was punished with a lonely eternity, is one of those major downers in the story. And Shannon, who used men to support her, and had little moral principles in doing so, was rewarded in the after life. Life is not fair.
