Although they got together properly after Vincent died, I always see the breakup of Booth and Hannah as the start for Booth/Bones. I liked the vulnerable moment that came with booth.. Quite simply, Booth never dealt with his feelings when Brennan turned him down. So when his Hannah-shield was taken away, Booth had to finally confront why his relationships didn't turn.

Bones Hannah And Booth Break Up
Hannah gently rejects Booth, telling him that she's not the marrying kind, and Booth breaks up with her. She reluctantly accepts the break up, and decides to move out of his apartment,.