Before she knew he was a clone and she just thought he was a plant who took his role very seriously, she'd taken to teasing him. He was cute and passionate and so very easy to rile up at times. After she finds out she feels sick. She's never really taken any sort of ethical stance on cloning, but something in her stomach twists and she knows deep inside that what Cadmus and the Light did was wrong. Wrong in the way she wants no part of, which is the real reason she first starts helping him out.
She never stopped flirting with him, but somehow on their crazy quest to find someone who probably doesn't exist anymore he starts flirting back. She agreed on the no killing rule and much to her own surprise sticks with it, even when there's no way for him to find out if she doesn't. Somehow it works. They break beds and walls and dozens of Cadmus labs, but they never find what he's looking for, what she's supposed to be looking for. Only she thinks she found it somewhere inbetween the anonymous hotel rooms and back alley information deals. She found Roy.
Not the Roy that he wants her to find though. They fall into marriage the same way they fall into bed, and with the same disregard for structural stability as everything else they do. He buys her new sai sheaths instead of a ring and she gets him a quiver. They sign the marriage license in some back water town in the middle of nowhere with only the office secretary for a witness. Their hotel is firebombed just minutes after they leave town, but the city hall is fine so the marriage goes through.
She's never been so painfully happy. It's a startling realization that she'd burn the world down for Roy. Even more startling when she looks at the line of over-the-counter pregnancy tests and realizes she'd leave Roy for this baby. This unexpected and unplanned, but already loved, baby. She's never known love to be easy thing though so she doesn't balk at doing what she needs to do. She cleans up, packs up, and leaves with a note saying It's been fun Lover, but a cat needs to wander knowing it's cruel, but unable to help herself.
She doesn't burn the world down, but she does burn down a few buildings with a few people inside them. She hunts down everyone who's ever owed her a favor and twists until they spill their guts. She even goes back to Gotham and all it takes is one cup of tea and her mother is calling in all of her old markers. She may have been out of the game, but everyone knows what the old Huntress did to Sportsmaster last time he showed up. If nothing else the cops still tell stories about coming into the apartment to find Robin laughing himself sick in the window as the escaped prisoner lay screaming on the floor from his busted kneecaps, Paula Crock holding her frying pan and screaming in Vietnamese at the man. No one dares to claim they don't remember who Huntress was and what she did for them.
Together they piece a tapestry of maybes and possibles and follow one thread to an almost positive. By the time her beautiful baby girl is born they have a solid lead. One last chance to find the original Roy. She'll give him this one last chance to put his demons to rest and become the father she knows he can be. The father their daughter needs.
Seeing him looking down at Lian she knows she made the right choices. She'd burn down the world for Roy Harper, but all it takes is that look of wonder in his eyes to know that they'd both burn down the entire fucking universe for that little girl.