Mass Effect 2’s loyalty missions can be filled with important decisions that players will need to make. These decisions can then impact the rest of the campaign, and even the events of Mass Effect 3.
During Jack’s loyalty mission, players will be helping her to confront her troubled past, exploring the facility that she lived in when she was a child. During a final showdown with Aresh, the player can attempt to convince Jack to spare Aresh.
This boils down to a Paragon or Renegade choice, and will mostly be impacted by how players are trying to play the game. As far as long term consequences, players who use the same save file for Mass Effect 3 will eventually learn that Aresh goes on to save a lot of live.
A bigger knock-on effect for this mission is that if Miranda is already loyal to you, she will argue with Jack when you return to the ship. If either your Renegade or Paragon points are high enough then you can Charm or Intimidate your way through the problem.
If not, and you side with Miranda, Jack will become disloyal, and if you side with Jack, the same will happen with Miranda. You can build the loyalty back up by using dialogue options that are locked behind high Paragon or Renegade scores, however.