After you get Yua, you should speak to Bosch at Viree. It should automatically teleport you and trigger the Trout's mansion part.
*Spoilers*
Failing to save Mina is a major plot point that will affect the game and lock you out of parts of the story but is a requirement to get the 4th ending where you recruit no one. It will just be you, Bosch, and Yua against the world. Basically you will take a boat from the rebel hideout to Evarai, but will not be able to fly at all in the game.