Note: If you go this route, then Morrigan will leave your party.
After "The Landsmeet" ends, travel to Redcliffe. You will find out what the fate of the Grey Wardens is. Morrigan will offer you the chance of going through a dark ritual the night before the battle. Refuse her. Then complete "The Final Battle". There's nothing special to "The Final Battle" other than surviving waves upon waves of Darkspawn.
Once you make your way to the top of Fort Drakon, the fun begins. This isn't quite the same as your other encounters with dragons. The Archdemon is much, much tougher. Plus, you'll have to deal with a few waves of Darkspawn that run out of the Fort. Call in support troops (see Defender for more details) to help out. There are also several balistas around the roof. Get behind one, push to rotate it so it's aimed at the Archdemon and fire away.