They should continue experiments in red lyrium, which unintentionally call the darkspawn to the Tevinter Imperium. Before they realize what's happening the country is invaded and they must call upon the aide of Weissaupt before the horde reaches the capital.
Crap. I could see what's left of both the Venatori and the Red Templars allying with the Wardens to come up with something awful. We've already seen one Tevinter mage pull the wool over the Wardens' eyes, and I don't think it was all due to Cory's influence. He knew where to hit the Wardens where it hurt the most, using the Nightmare and Cory's magic as well as his own cleverly chosen words. If the Architect is alive, he's likely to be involved. If not, I could see one of the darkspawn he "awakened" getting involved. It won't be another ancient magister, but a different set of darkspawn troubles.
The Wardens want to stop the Blights at any cost, and the last time an Awakened darkspawn got involved, the Fifth Blight happened. It was a magister yes, but he wasn't nearly the powerhouse that Cory was. He was just very smart, and was creative as well as articulate. A pretty dangerous combination, and who knows if there is some Awakened darkspawn out there that thought that the Architect had the right idea. The Wardens have been proven to be very vulnerable through the duty and desire to end all Blights.
No doubt in my mind. We'll end up in the Anderfels and in the Deep Roads soon enough. Why? To make sure all three groups don't kick start another Blight too soon in the series.