Not long after the Clone Wars starts Obi-Wan ends up getting his lover pregnant. She was going to keep the baby but after giving birth plans changed. Obi-Wan just found out about the baby, he definitely knows it's his but he's at a loss what to do. He could give his kid to a loving family or take the child to the Jedi temple...but he's formed an attachment. Whatever he chooses the option will hurt him. Anakin and Padme find out and decide to come clean about the marriage. They adopt the baby but in the process end up in another secret relationship with Obi-Wan.

Anakin/Obi-Wan/Padme