Mass Effect 2 loyalty missions can be filled with important decisions that players will have to make. These decisions can then affect the rest of the campaign and even Mass Effect 3 events.
During Jack’s loyalty mission, players will help her face her turbulent past and explore the facilities she lived in when she was a child. During the final showdown with Aresh, the player may try to persuade Jack to spare Aresh.
This boils down to the choice of Paragon or Renegade and will usually be affected by how players try to play the game. As for the long-term consequences, players who use the same save file for Mass Effect 3 will eventually learn that Aresh continues to save a lot of live ones.
The bigger effect of this mission is that if Miranda is already loyal to you, he will argue with Jack when you return to the ship. If your Renegade or Paragon points are high enough, you can solve the problem with magic or intimidation.
If not, and you take Miranda’s side, Jack will become disloyal, and if you take Jack’s side, the same will happen to Miranda. You can create loyalty back using the dialog options that are locked for a high Paragon or Renegade score.