After saving either Amaranthine or the Keep, you'll be told where the Mother's Lair is. If you saved the Keep, it's "Lair of the Mother" on your map. If you saved Amaranthine, it's "Dragonbone Wastes" on your map. Whatever it's called, it's the only available location, so head there. Fight through the Darkspawn civil war, which includes a High Dragon. After the dragon is defeated, enter Drake's Fall. You'll have to make a choice of whether to help The Architect or not. Helping him gives you more help for the fight against the Mother. In Drake's Fall, activate the three towers by finding the 12 crystals. These are dropped by enemies, in chests or in flesh pods. The towers will give you another method to fight the Mother. Enter The Nest after making your way down. The Mother is very much like the Broodmother from Origins. Fight her the same way. Once you're done, ding!