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Felicity had loved Billy. Or she was close to loving him. Or she thought she loved him. Regardless, she was heartbroken when he was killed. But she didn't know if it was because he was the man she loved or if it was because he was a good person who didn't deserve such a horrible death. Or death at all.
Her confusion over her feelings for Billy and his death only made her feel more guilty. It drove her to become single-minded in her quest to bring down Prometheus, turning her into a person who was beginning to lose her moral and ethical grip.
Once so sure about right and wrong, Felicity slowly slid into a grey area. She did what needed to be done, damn the consequences.
She knew Oliver and John were trying to reach her, to get her to think about what she was doing, but she didn't care. She remembered John telling her a long time ago that he didn't think there was a thing on this planet that could make her a bad person, but she was starting to think he was wrong.
Then Oliver was kidnapped and it threw her into overdrive. She wanted to kill Adrian Chase with her bare hands. He had murdered Billy and deeply hurt one of her teammates.
She was furious when Oliver not only wouldn't see things her way, but tried to stop her from carrying out Helix' mission. She would have argued with him over it until the end of time, but there was a sudden flash in the lair that put her, and Oliver, in danger.
They had to get out before the gas built up and exploded. Both were stubborn and there was still some distrust, but working together soon had them dropping their guards. Without use of her legs, Felicity had to rely on Oliver and he needed Felicity's genius and her determination.
Over the next few hours, they learned some lessons about themselves and some hard truths about each other. There was a part of Oliver that still believed he didn't deserve happiness. And Felicity still stood by him, arguing for the goodness in him. The hard year of trying to work together without being together began to melt away.
By the time Dig pulled them up out of the darkness of the elevator shaft, the truth was clear. They needed each other, and their team.
Now that she had some perspective, Felicity realized that she struggled with guilt over Billy because she had always been in love with Oliver Queen. Even when she thought she was moving on from him after their breakup, her love for him permeated everything she did. From the moment they met, he was part of her, and that feeling only grew with time.
Now that they had talked about the problems that kept them apart and had begun to rebuild their lives together, she was feeling more grounded. She would never be the same, though. Havenrock and Prometheus made sure of that.
Maybe this was better, though. She now understood what drove Oliver to make decisions alone and he realized what it was like to watch the person you love go down a bad road and not be able to stop them.
Felicity had spent over a year trying to break free from Oliver, but the first time they made love since their ill-advised tryst in the lair, Felicity knew. She knew that she would never escape loving Oliver Queen and, finally, she didn't want to.