Further speculation on the nature and ultimate power behind The Silence.
One issue with the Omega theory is that, acting alone, could he really marshall a force as large as has been sent against The Doctor? I’m not sure. He’d get a follower here, a follower there. And inspiring them to hate The Doctor on his word alone? When they have little more than legends to go on?
Bringing a well organized group that already has information on The Doctor, that already hates him, and has a stronger cultural connection to the people he needs for his army? This would be a godsend to Omegas dreams of revenge.
Enter Torchwood 4. It’s at least possible that Omega could have learned about Torchwood when he visited Earth during Arc of Infinity. He could have set up Torchwood 4 as the nucleus of his backup revenge plan, and been responsible for removing them from Earth and possibly even their native time.