Why she did it? She didn't even really know why herself. All she knew was she saw Ford standing in the hallway, gun pointed at Marlo.
Andy and Sam had a moment of clarity before she found herself laying on the floor of 15 Division, hand gripping her now bleeding abdomen. "Andy, I want you to be happy more than anything in the world more than anything I could ever want for myself, and you are; with him." As he spoke those words she realized two things, that she wasn't in-love with Nick, it was easier to be with him, yes but her heart was still with Sam, and it probably always would be. And the second thing was that she wanted him to happy too, even if it was without her. It would break her heart everything she saw them together, but it would make her feel better knowing that he was truly happy.
So why she did it, why did she throw her arms in the air, pulling Ford's eyes and aim in her direction? Because she knew Sam was happy; without her and she wasn't about to let the one thing that made him happy get shot. So she called his name, and he pulled the trigger, he didn't miss like last time in the park. One shot, in the stomach, and god damn it hurt.
She selfishly chose to be Ford's target, because she realized that Sam didn't need her anymore, and that terrified her. She felt like her purpose in this world was unknown, sure, Nick needed her, but it wasn't the same. She didn't have to fight for her relationship with Nick, it just happened. But with Sam it was a battle, a struggle, confessing her feelings and him disappearing undercover. Then her finding him undercover and 'trying' to be normal together. Jerry dying. Her leaving for Dakota. It was always a fight for them to try and make it work, Sam would be in and she'd be out. Or she would crave his protection and he would still be searching for stable ground between them.
What she didn't realize was that Sam would chose her, after she feel to the ground; he ran to her. He didn't check on Marlo, he went to her side. Telling her to relax that everything was going to be okay, even thought he was terrified of losing her; for real, forever.
And all Nick could do was watch, watch the woman he deeply cared for in protective arms of the man she truly loved.
She didn't take the bullet to save Marlo, she took it for Sam. So he could be happy, but he could only be happy with her.
Their ride to the ambulance only confirmed that more, Sam had never been one to show his emotions but this was potentially the last time he'd ever be able to say anything to her and he wanted to say everything he had been thing over the past year, "McNally, you're... you're going to be fine. You're a fighter, and for once I'm going to do the talking." She nodded, without speaking. "I'm going to uh, tell you a story, one night after a really terrible shift, you had fallen asleep and uh I couldn't get my mind off the case, so I just was just laying there, you know, trying to sleep and uhh.." He reached his hand out and wrapped it in hers, "You looked so peaceful and at ease, and then all of a sudden you slowly opened your eyes, and just smiled at me. You leaned and wrapped your one arm around my neck and kissed me, it was like you knew I needed you, and you woke up just to make me feel loved and okay again, right then at that very moment, I knew, that you could make any day I can better. Any terrible day, an amazing one with one kiss. I know it's mushy. " She opened her mouth, "That was a pretty good story," He knew that what he needed to say next, "I love you, I love you Andy McNally, you're my story McNally, you." He didn't know if she was too weak to answer or not wanting to ruin this amazing moment, kissing her on the top of the forehead before they took her out of the ambulance.
Sitting there all he knew was he was in-love with her, and he had no idea why she took the bullet for Marlo.