My own half baked suppositions:
Perhaps, when Susan Baker married James and James wanted custody of his two children, Susan was not so thrilled. Suddenly, the married man I am having an affair with is mine, wife is finally out of the picture, I will have him to myself and we will start our own little family. Then James ruined that by pursuing custody of his kids. Now Susan is sadled with two kids she resents. So she is physically abusive with them. Maybe things got carried away with Paul and then she's a murderer. Who knows if James was involved either before or after the fact but the body must be dealt with.
Flash forward 20 years. Susan was never blessed with children of her own (karma?) and she befriends Shannon's parents and begins babysitting. She may have developed an unhealthy attachment to her. Giving her all the love (scary I know) and attention she imagined she would have given her own child.
She sees these young parents struggling, not parenting the way she believes they should. She begins trying to get the baby removed from their care. That is unsuccessful. Tina confides how hard it is, how much she wishes things were different. Susan tells her things could be different. They cook up this crazy abduction hoax to explain baby's absence when Susan in fact has the child all along.
Then WS gets involved and digs up the old baby Paul connection and forwards info to LE. They suddenly see her as a person of interest and the focus of the investigation swings to her. Uh oh. Now what? So Susan begins scrambling to figure a way out and starts finger pointing at mom.
Thankfully, baby Shannon is found and ALIVE and well. I wish this child stability, love, and happiness. What a rocky beginning for such a sweet little angel. Welcome back Shannon

Best wishes from all of us baby girl.