She didn't get on the boat. The moment she fired her gun, the moment Henry was finally dead, she knew she couldn't go home. Not now, maybe not ever.
Instead she paid another woman to get on in her place. Annie knew Auggie and knew that the captain would be instructed not to leave without her. So she found a woman in need of money who could easily pass as herself, and paid her to get on that boat, sliding her phone into the woman's bag in order to avoid being tracked. She knew Auggie would be keeping an eye on her GPS, and by the time he called and figured out she wasn't on that boat, Annie would be long gone.
This mission had changed her. Annie became a person she wasn't proud of. She put the lives of innocent people in danger, including that of Jai's mother. She tortured to get Intel. She even slept with or drugged some, sometimes both. And she ran. She never stopped running. Even with Henry dead, she would never feel safe.
Annie knew that Henry sent out a picture, but who received the picture she did not know. What if he had plans in motion in case of his own death? Knowing Henry, this was probably the case. If she went back home she would be putting everyone in danger, Auggie most of all. She knew he would do anything to keep her safe, including giving his own life. He had given up so much for her already, and she couldn't risk putting him through any more.
Annie knew that the moment Auggie realized she wasn't on that boat, he would be looking for her. He would be hurt, and she knew that, but he would also be safe, and that was what mattered. She needed to go somewhere no one would find her.
Annie thought back to the day she and Simon were shot. She was ready to pack up and run away with him, until she saw the picture of her family, reminding her what she would be leaving begin behind.
Simon promised her a place where they could live in peace and never have to worry about being found. Maldives. When he realized she wasn't coming, before being shot, he handed her a slip with the coordinates on it, hoping one day she would change her mind and join him. She memorized those coordinates in case of emergency, a time like this. This is where she would go now.
Annie needed to act fast. She knew she couldn't leave without saying goodbye to Auggie. Before sending the woman on her way, she composed an email to him, setting it on a 12 hour timer. By the time he got it the agency would already know she wasn't on the boat, and she would be gone. There was so much she wanted to say, but not enough time. So she looked to the words of an old love. Words that had once kept her up and night trying to understand their meaning, and words she wished she listened to.
Annie put the phone in the woman's bag, and sent her on her way. She quickly found he way to the airport, and using an untraceable passport she had made for her earlier that week, she flew to Malaysia. "By now they should know I'm gone" she thought.
There Annie found a man with an old fishing boat, and paid him more than it was worth to buy it off of him. She knew people from the agency would come down to the dock looking for her, so she asked him to lie. He agreed, seeing she was obviously in pain. She thanked him and went on her way.
"Maldives, here I come," she thought.