TimKon Not-So-Clone-Baby au:
Tim and Kon are older here, like in their 20s. They've been married for 2 years and together for the past- since they've been 18(No Bernard). Since they're a good age and have been married for a bit, they decided to adopt a baby.
They go to the adoption agency in Metropolis and they adopt a baby girl after filling out a bunch of paper work and going through everything. She's 6 months old, has black curly hair, and the brightest blue eyes you ever did see.
They wait about a month before introducing her to their families, that way they have time to adjust having her as a part of their small family now.
They don't know who, probably Jason or Dick, jokes about how she looks awfully similar to them. And Bruce, the paranoid person he is, takes a blood test of her. Not only to see her parentage to see who would give up such a perfect little girl, but to also see if she'll have any short comings in life.
That's when they find out that she, is in fact, the daughter of Tim and Kon. They have no idea how it happened, or why she was even in an orphanage or going to be adopted out.
It takes a long time and a lot of digging to find out that Cadmus and Luthor were at play here. Turns out they found out Red Robin's secret identity and cloned him and Superboy together to create a perfect clone with Red Robin's intellect and Superboy's powers.
They take down Cadmus, again and once and for all. They also get rid of any genetic information they have of the two of them and anyone else so it never happens again. They also track down the dejected Cadmus agent that put the baby in the orphanage to find out more.
They find out he did it so she'd have a normal life, not realizing if she had gone to someone else and she awakened her powers something bad could've happened.
Optional/Alternative idea:
The scientist also reveals that there were others that he helped "dispose" of that went to orphanages. They all vary in ages, but Tim and Kon take them all and end up with a pretty big family. They couldn't be more happier.