Spoilers for Forging Bonds
What I think is that while Kate did love Neal, she was being used as a pawn by Adler. Adler knew that Nick was Neal, he'd already seen it in the paper if he didn't know already. Neal conned Adler for his account password and then I think Adler told Kate to delay Neal so that he did not make the transfer. Then Adler set his plans in motion to disappear.
Skip ahead and Fowler approached Neal about the music box. I think Kate knew it was Adler. When Peter confronted her, Kate loved Neal but was under Adler's thrall and made plans with Fowler to escape. Adler had the plane blown up early in order to kill Kate for defying him. He wants to get control over Neal to have him work for him again.
Just my idol speculation when I should be working.
Skip ahead and Fowler approached Neal about the music box. I think Kate knew it was Adler. When Peter confronted her, Kate loved Neal but was under Adler's thrall and made plans with Fowler to escape. Adler had the plane blown up early in order to kill Kate for defying him. He wants to get control over Neal to have him work for him again.
Just my idol speculation when I should be working.