According to sources, Tom Cruise has had zero contact with his daughter since Katie Holmes divorced him in 2012 and left Scientology. And apparently Tom's done being apart from Suri. He knows better than anyone Scientology will do just about anything to stop this from happening. According to The Star:
He has reached the breaking point, and something has to give. If he wants her back, he’ll have to walk away from the church, which has been a huge part of his life, to say the least.
Leaving Scientology would be the toughest decision he’ll ever have to make! If Scientology declared open season on Tom, they could bury hum, since they’ve probably got all sorts of dirt on him from his audit sessions.
It’s an unspoken threat, but Tom has to be aware that the church would do everything in its power to keep him from leaving.