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At first, Amy was mad at Jake. For a lot of things, actually, not just one thing.
The first reason is for leaving her. He had agreed to go undercover with zero hesitation, and didn’t even consider how it would make her feel. That seems harsh, she realises, that it’s his fault for leaving when it’s his job and his life. Who is she to tell him what to do?
The second reason is for leaving like he did. The last conversation they shared included him confessing feelings to her, and then promptly walking away. She hadn’t been able to say anything back. She hadn’t been able to Tell him that she had also been thinking about that stuff recently, too. He didn’t give her a chance to say anything.
She was mad that he had chosen that moment to say those words to her. He had had so much time over the past, what, weeks? Months? However long he had been feeling like that, he could have mentioned it, and she could have had some thinking time and been able to make a decision. But no, he told her on a random evening after a long day of work, right before he’s due to go undercover. For god knows how long.
Those feelings of anger churned away inside her for not much longer than a month. It’s been replaced, slowly, by feelings of loneliness and sadness, moments of staring across her desk at his vacant seat, where his energy and conversations and jokes used to light up the precinct and make it feel more alive. Now, in contrast, nothing exciting seems to happen, and it may just be coincidence but she’s fairly certain a it’s because of his lack of presence. Times of wondering how much longer she’ll have to suffer this time apart.
Amy misses him, she’s come to realise. She misses him more than the others, and more than she thought she would have done. Maybe he’s just getting in her head from all the romantic-stylez confessions, but her feelings for him have…changed. She can’t quite understand why or how, but they have.
Amy misses him and she wants him to come home, she really needs him home.