I'm writing this section assuming you went lightside. If not, you'll have to fight all the Jedi as well as the cultists, making it twice as difficult given that the Jedi have protection, absorb, and heal. There are also a few places where duelists are substituted with Jedi.
Use sense to find the nearest enemy. He should be a lightstaff wielder. Help your friends kill him and then proceed further into the crypts, helping other Jedi you meet along the way. Eventually you can take a left turn. Do so and enter. You should have a total of four Jedi with you if you saved the two along the way. Use absorb to negate push and pull. When there are no more enemies remaining, push the statues to open up a hole below. Use absorb to kill the cultist along with his duelist friend. Head down the stairs. On the way you will meet a lightstaff user. Finish him quickly. Run down and help fellow Jedi with the duelists. Go up to the door with a triangular window in it. Use force sense to see the symbols you must push. There are only three symbols. Head down with force absorb ready to kill the cultist and his pal the duelist to the left and the cultist to the right around the pillar. Return to the entrance. Pull the discolored rocks and use them to jump on top of the pillar. A dualsabered duelist will attack, kill him and jump to the very top of the pillar. Jump to the nearby platform and head down. Along the way, two duelists jump in from the sides. Kill both with rolling stabs and continue down. Help out the Jedi take on the single duelist. Look for a huge hole in the ground which you can enter. Avenge the Jedi in the tunnel and pull the duelist as he retreats. Continue into the next chamber where there are two duelists and a cultist. Explore the lower level. You should come upon two more duelists and a cultist. As soon as you defeat these three, another pair will come rushing in. Use absorb against the cultist's lightning. Proceed into the next area and help out against the cultists. When you're finished, head for the carving with a hole in it. Enter. Checkpoint! Drop down from beam to beam, and look for an opening you can reach. Now go up and jump into the room. A cultist is to the left, and a duelist is across the room. Kill both and then take the exit down. The next room holds two duelists. Again, use absorb and protection. Go down further the path to a room filled with lava. Use the stairs and jumping blocks and get to the other side. Upstairs are two duelists to the right, and a cultist to the left. Kill the cultist first. Then use absorb and protection to wipe out the two duelists. At the end of the room, two more duelists with lightstaffs drop down, and a dualsabered opponent from the right. Kill all three and then break the supports to the stone block in the back of the room. Return to the room where you had to use sight and push in the proper blocks. Remember the steps? Go back to the room where you had to drop from beam to beam and then jump back up. The door you opened by breaking those supports is at the opposite end of the panels you had to push. A lightstaff user and a dualsabered opponent will rush. Another lightstaff duelist will appear, one of those insanely supreme force users. In all likelihood, he'll kill your support (if you went light) so you'll have to finish him off. Exit through the door to end the level. Note: If you went dark, just avoid most of the fighting between the duelists and Jedi and just go for final door after you broke the supports.
I am also writing this section on the premise that you went light. If not, its still the same path. Just you'll have to kill everyone, and I mean everyone to get there.
As soon as you start, kill the dualsabered duelist outside. Head down the ramps and slide off the structure to the sand below. Walk left. Along the way you'll face several enemies. When you see fighting in the distance, move it. Walk down to the rock and use it to jump across to the other side. The other side holds one of the dark masters as he takes on three of your fellow classmates. In all likelihood, they'll all be dead. Use absorb and protect. When he's dead, push the crumbled part of the pillar and use it as a bridge. Snipe the cultist, the one closest to you. Then kill his partner. Slide down the pit using the column below. Enter the structure on the left. Jump from rock to rock to get to the top most level. Peek out to the left. Mind trick the stormtroopers and then jump over to get their attention. Mind trick everyone you can and then kill them. Weave between the shuttles, killing the cannon fodder as you run along. Help out another Jedi with the two duelists and cultist. Backtrack to the tomb with a statue on top. Go up the long flight of stairs. A lightstaff duelist is waiting. After he's defeated, head down. A dualsabered duelist will attack. After he's dead, enter the great hall. A cultist is to the left and a duelist to the right. Continue along the walkway. Ahead are two more duelists, a staff user and a dualsaber opponent. After they have been defeated, head into the final room. You will first fight Tavion. She uses the staff to shoot you but you can jump over the beams. Or better yet, use speed and cut her up as she tries to keep up with you. After you've defeated her once, she'll infuse Ragnos with the power of the staff. His spirit will leave his body and possess that of Tavion. S/He uses a sword infused with the power of the dark side. S/He doesn't seem to use any force powers, just the sword. Eventually you'll have hurt it enough and the game is done. Enjoy the ending cutscenes where you reunite with Rosh and are given praise by both Kyle and Luke. Congratulations, you have beat Jedi Academy!
Your first duel with Tavion is much the same if you went dark. This time around she uses the staff not as a laser of sorts but like some sorta hammer which will knock you go the ground. Same strategy as before though, cut her up as much as possible. Except this time you cut Tavion down in the first encounter before she even wakes up Ragnos. The second fight of the hall is with Kyle. One of the reasons I picked dual sabers instead of staying single bladed or going with the staff was because I knew that Kyle could pull your lightsaber away. If he pulls your staff or your saber away, you are completely defenseless. However, if you have dual sabers, you still have a lightsaber to deflect his attacks with. Use what force powers you have, in addition to speed and Kyle will eventually be defeated. You have turned to the dark side! Good for you! You end up flying to the Star Destroyer, killing the Admiral, and taking over the ship. The Imperial March theme plays during the credits.