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Quarles sent one of his men to knock off an oxy clinic run by Boyd. Limehouse's number two had already set in motion a separate attempt to hit the clinic, and one of the girls in that hit witnessed Quarles' successful attempt.
When Raylan investigates it, Boyd tells him where Quarles' own oxy clinic is being run, so he heads out there. He attempts to take out Quarles' man, but doesn't get to him. Quarles enjoys that he now knows Raylan and Boyd work together.
Winona left Raylan because she knows he's never going to change or move. She loves him, but she knows it's never going to work, so she goes out to her sister's.