To the vast majority of viewers, it made no sense.
Throughout the series, Sayid was shown pining for Nadia, a woman from his home land. A woman for whom Sayid tortured, then let escape - - - turning himself into a cold blood killer (by taking out a superior officer to allow her to escape.) After the war, Sayid spent his entire life trying to find Nadia, considered by all to be "the love of his life." He went so far as to work for the CIA, a dirty deal to double cross a childhood friend in order to get a chance to meet Nadia. So, Sayid was deeply in love with Nadia.
But that is just one side of the story. Sayid's attraction and affection for Nadia was clear. But what was Nadia's true feelings toward Sayid. As a child, it would seem she had a crush on Sayid. Even in the school yard, Sayid was different: strong and a provider. But when there was political change in Iraq, Sayid would wind up on the other side: with the Guard, while Nadia and her family were in the rebel camp. This basic ideological divide would doom most couples.
But even when Sayid was ordered to torture her to get information about the rebels, Nadia seemed to forgive Sayid. As a result, Sayid's heart overwhelmed his training and rank to allow her freedom. However, some could argue that Nadia was using her past relationship to manipulate Sayid to grant her freedom - - - a ruse, a classic spy move - - - not out of love but necessity.
But the latter evidence seems to contradict this faux spy story. When Sayid was rescued as part of the O6, he was met at the airport by Nadia. They embraced. They began to start their new life together in LA. Now, various theorists don't understand how this even happened . . . why the airline would find a stranger, such as Nadia, to greet Sayid in Hawaii is a mystery. Perhaps the CIA knew her whereabouts under a protective custody program, but not an airline.
One theory has it that the O6 never made it to the awkward press conference in Honolulu. That when the freighter was blown up, the survivors were in bad shape. Penny's boat was actually a trailing shadow craft to pick up survivors for Widmore so as to reprogram the brains in a virtual reality "rescue" so as to have them volunteer to return to the island to fight Jacob/MIB. If Widmore could "fake" an underwater crash site including passenger bodies, then he could easily brain wash island survivors.
When Nadia was killed by a motor vehicle in a cross walk when Sayid was pulled by Jacob, Sayid was totally lost. He had lost his one, true love. He was a broken man. He could never love another woman. He turned into a zombie - - - easily manipulated to become Ben's assassin under the guise of getting revenge of those who killed Nadia. (This also shows a direct link between Jacob's influence to Ben's missions with Sayid.)
Even back on the island, Sayid never forgot about Nadia. So it was a shock to find Sayid winding up with Shannon in the End. They only had a week long island affair. It was spurred by a matter of convenience and loneliness. Shannon's brother, her one protector, had died. Sayid was still seen as an outcast within the group. Shannon was in need of finding someone to take care of her since she was accustomed to the life of luxury. She used her one commodity, her beauty, as currency to find another man to be with her. But when she was killed in the jungle, Sayid was cut down to his core in emotional grief. Some think that Sayid's physical relationship with Shannon could have clouded his long term memories, or that he was actually re-living the terror of losing Nadia all over again.
Sayid was doomed at that point. Any woman he loved would die in his arms. He thought it was his fault. He could never love again because the pain was too great. In order to cut out the pain, he had to cut out his own heart - - - die and be reincarnated as an empty soul.
But when the cast was reunited in purgatory/heaven of the sideways world, the image-character of Nadia was present. But she was married to Sayid's brother, who was in trouble with the mob. Sayid had to "fix" it - - - to make Nadia happy. It was like the one woman he loved he could never have - - - but there was no evidence of that in the "real" world. So in that respect, Nadia's soul must have bonded with Sayid's brother while she waited for him to show up in the next level of existence. That must have paved the way for Sayid to release his feelings toward her, opening up the possibility of finding his second love, Shannon. But that is a weak appraisal of the overall Sayid-Nadia story line.
A week of passion with a different stranger is more important than a life long longing over a love that you finally found after years of searching? Sayid and Nadia were together in LA. They were happy. They went to Hurley and Sun's parties. So why did that love and affection carry over into the next world?
Sayid and Nadia's relationship was troubled from the beginning. He was a soldier, she was a freedom fighter. He was a poor boy, she was from an upper class family. He was repressed by his emotions, she was outgoing in her beliefs. In a world where opposites attract, they would be a perfect pair. But in reality, opposites often cause conflict in their own relationship. Deep, lasting relationships have as a foundation core similar values, goals, beliefs and mutual dreams. Perhaps Sayid's feelings toward Nadia were a dreamer's lust for something that could have been instead of actual love.
And in that regard, Shannon was the only person Sayid knew who loved him for what he truly was - - - she knew his background, she knew about all the bad things he had done, but she still took him in and loved him. Even that short term bond between two troubled souls could have a lasting impact.
