Playing through SW-TOR, from time to time, I would encounter nasty surprises, where the game would force me to use a companion that I had not equipped properly, or take away a companion to which I had given my best equipment.
To aid other players (and myself, if I choose to re-play some of the stories), I would like to catalogue these instances, and attempt to avoid as many spoilers as I can in the process.
- Sith Inquisitor
- Sith Warrior
- Before Coruscant: You must fight Malavi Quinn (I don't know if how you've geared him affects anything)
- Bounty Hunter
- Imperial Agent
- Entirety of Corellia: Removal of Kaliyo
After Voss, the mission "Road to Ruin" calls you to Dromund Kaas, where some Imperial people arrest Kaliyo. She returns to your party at the start of the your final Agent mission (to conclude Chapter 3): "The Star Chamber".- Jedi Consular
- Jedi Knight
- End of Chapter 1: Must use Kira
For the Mission "Fate of the Jedi", you must use your Kira Carsen companion to at least start the boss (Darth Angral) fight. You can run away and then summon a different companion if you'd like.- Final part of final Mission (end of Chapter 3): Must use T7-O1
To face the Emperor in the final JK mission, "Doomsday", you have no choice but to use T7 (or no companion).- Trooper
- Final Mission for Chapter 2: Lose a companion for a period of time after the mission. Must use Yuun and Tanno Vik during the mission.
For the first half of the Mission "Battle of the Gauntlet", you must use Yuun. You don't even see your companions as "Unavailable" - at this point, you have one companion in your crew list. For the second half of the mission, you must use Tanno Vik.
Also, in a dialog ahead of the mission, you choose two companions out of Elara Dorne, Aric Jorgan, and M1-4X. Depending on the combination you choose, one companion will suffer an "injury" and you will lose the use of that companion for a period of time (on the order of hours, I think). If you pick Forex and Jorgan, you lose Jorgan. For any other combination, you lose Dorne.- Smuggler