It was never actually about Lincoln! It was about Michael. They knew Michael would break Lincoln out of prison. The Company must already know Michael is a Genius. It's like they're testing and experimenting on him. If you listen to that General Man towards the end of Sona, he says "We're counting on Schofield escaping." They don't really need Lincoln anymore, what would be the point? It's all about Michael's abilities. They're just toying and experimenting with him. If you watch Sona again carefully, you'll realize. I also believe Lincol & Sara are going to try and break Michael out of prison. Did anyone catch on the fact that Sara is in danger. Some man was following her at the end and Linc couldn't find her.