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Your goal here is to first enter either the Trayus Crescent via an exit on the west side, or the Trayus Proving Grounds via an exit on the eastern side. Once there, you'll enter back into the Academy at either #6 or #8 and wage your second to last battle at #7. To avoid backtracking, it's advisable to do Trayus Crescent first, head back here to defeat your opponent at #7, and then clear out the Proving Grounds, stopping by the workbench there, before finally coming back and exiting up to Trayus Core at #10 for your final battle. I'd recommend going to both the Crescent and Proving Grounds for additional experience, even though only one side is required.
Trayus Academy is literally littered with Sith. If you have the Immortality Belt, with damage resistance, it is immensely helpful here. You'll have to battle Sith Assassins, Apprentices, and eventually Sith Lords, Marauders and Dark Jedi before it's done. If you played the first KotOR, however, this is absolutely nothing compared to its final stages, so rest easier. You are easily powerful enough to take on anything the academy throws at you, almost in fact mowing down the competition by this point, regardless of their title.
1 - Exit
Exit to Depths (#8)
. As soon as you enter, you'll do battle at #2. See below.
2 - Elite Sith Assassin
This Elite Assassin is slightly tougher than most, but probably not quite so much as the Greater Storm Beast you recently fought.
3 - Exit
Exit to Trayus Crescent (#1)
4 - Exit
Exit to Trayus Crescent (#2)
5 - Exit
Exit to Trayus Crescent (#3)
6 - Exit
Exit to Trayus Crescent (#9)
7 - Darth Sion
When you reach this point, Darth Sion confronts you. This battle takes place in three phases. Each conversation with him has a chance of reducing his Will Saving throws, Constitution and Wisdom modifiers. In the first conversation, you can lie/persuade by saying you do not have to do battle. In the second conversation, persuade him that Kreia is just using him to again reduce his stats.
If you are a consular with very high wisdom, even Sion cannot resist your force attacks such as Stasis Field. In an example, as a Light Side Jedi Master with Enlightenment, Sion had to go against my DC of 60 with his maximum 57 (Base 37 + 20); there was no way he could stop it and it of course made the battle incredibly easy. If you do not have high wisdom, simply use your Verpine Prototype Shield(s) for protection and hit him with your best melee feats. Energy Resistance can help as well.
8 - Exit
Exit to Trayus Proving Grounds (#1)
9 - Exit
Exit to Trayus Proving Grounds (#2)
10 - Exit
Exit to Trayus Core (#1)
. If you haven't yet been to the Workbench in the Proving Grounds, going there now will be your last chance before you enter into the final battle.