She later joins the Ebonheart Pact and is encountered a few times aftrewards at various places across Morrowind and Skyrim, such as Ebonheart, where she is inconsolable. Note that she can be found regardless of choice during Crossroads, as she was not an active participant in either quest.
The Daggerfall Covenant has assaulted Bleakrock Village, and Captain Rana has sent the surviving refugees to Last Rest, a tomb near the town. Rana and the Vestige must clear the tomb of Draugr so that it can safely house the refugees.
Later on, Aera can be found in Bal Foyen.