The Jedi Academy Game is a tie in that goes in all directions. By this I mean previous games, comics and books, as well as those that come after. For that alone I would love it. I also find it most helpful in that I had previously been stuck on Jedi Outcast. After playing this I found it gave me skills I needed to succeed at the earlier game.
Released the year after Attack of the Clones, it is a follow up on the popular ‘Dark Forces’ series. In this game, instead of playing Kyle Katarn, you play his apprentice, Jaden Korr. As you work up through the levels, you start out choosing whether to play male or female from 4 species and what styles to wear. You also get to choose from different lightsaber hilts.

The opening encounter introduces Rosh Penin, a fellow student and involves a shuttle crash onto the Yavin moon. We quickly find trouble at work in the form of Imperial allies who have dark Jedi companions. This sets the story for the game. We also learn Jaden does already have at least some skill in the Force: already has built a lightsaber with no training.
The very important detail to continuity comes in the form of Jedi Master Luke Skywalker assigning students to teachers. He explains that the ‘old’ Jedi Order kept it one on one, but they did not yet have enough Jedi for that. This explains that this is not a contradiction with the Phantom Menace and Attack of the Clones, (Revenge of the Sith wasn’t out yet) but a natural result of a decimated order. As he assigns students to teachers, familiar names from the Jedi Academy books are among them.

The first level is an awesome tie in level. Jaden gets to run through the Yavin Academy and solve puzzles as the player learn about using the Force and the lightsaber. We get the basics immediately: push, pull, speed, jump. Some of this scenery we experienced in Jedi Outcast. And previously we had to earn (or re-earn) those powers. But it also ties in to other stories. This is what Jaina, Jacen, Anakin Solo and their friends would’ve gone through between scenes of the Young Jedi Knights and Junior Jedi Knights books.
Having warmed up, we are now ready to take on missions. We get to choose our weapons and which Force powers to boost first. Here we get to choose which order they come in. On one, we get to team up with Chewbacca. Some of the missions are just good deeds, others are a quest to find out why the Empire was sneaking around Yavin 4. We meet sandpeople, jawas, pirates and (of course) imperials.
Tie ins in the first set of missions: (Jedi Initate)
Emergency Assistance – Bakura: is set on the world introduced in the Truce of Bakura by Kathy Tyers, first novel after the Thrawn trilogy.
Cult Investigation – Corellia: We’ve long heard Han Solo was Corellian, but the movies never showed it. It has popped up in Rogue Leader & X-Wing Rogue Squadron comics, I,Jedi and the Corellian trilogy novels. It is a hotspot in the Legacy of the Force novel series. We admittedly don’t see much outside of the flying tram.
Nod to another franchise:
Merchant Rescue – Blanjeel was inspired apparently by the Dune series.
Tie ins in the second set of missions: (Jedi Apprentice)

Vjun – Exterior / Vjun – Castle Basement / Vjun – Vader’s Castle : the planet Vjun was first revealed in Dark Empire 2 comics and visited by Anakin Solo in Junior Jedi Knights, Vader’s Fortress. The planet was also base to Dooku in Yoda: Dark Rendezvous.
Now we need to choose whether to add a new style of lightsaber combat. Or we can choose to stick with what we got but choose duel lightsabers (pick your hilts and colors) like Anakin used in Attack of the Clones, or a double bladed saber, such as introduced by Exar Kun and later used by Darth Maul as well as Bastila Shan.
Chandrila – This is a massive undergrown tomb of a great Jedi, The Bar’sen’thor. This is the Jedi Consular story arc from Star Wars the Old Republic.
Tie ins in the third set of missions: (Jedi Knight)
Dismantle Device – Yalara – This level features the Noghri, made famous in the Thrawn trilogy. These noghri have been out of touch for awhile. They are not allies, even though they are fighting Imperials and will attack with poison gas.
Force Theft Investigation – Byss : The planet Byss was first revealed in Dark Empire comics. It was destroyed in Empire’s End comics. It is the destroyed system that is visited in the game.
Taspir (which is all new) is where you are faced with the test of rescuing Rosh Penin, fellow student who (apparently) was captured and turned. At this point you have to choose whether to forgive him (and stay in the light) or kill him (and go to the Dark side.)

Korriban – Catacombs / Korriban – Valley of the Dark Lords : Korriban first appears in Tales of the Jedi, comics. It reappears in Empire’s End (comics), Knights of the Old Republic (game and comics), The Old Republic (game and comics), Legacy of the Force, Fate of the Jedi, Jedi Quest: The Final Showdown,Crosscurrent and Riptide (both of the latter starring Jaden Korr).
Somewhere in the third set of missions you have to choose to stay a Jedi of the Light or fall to the Dark Side.
For a real walkthrough, Check out this Gamespot article.

Each video game has one ending which is considered canon. In this case, it’s the light side ending. While Jaden Korr can be played with various options, the canon version is a white human male since that is ow he appears in the follow up books Riptide and Crosscurrent. (Which is a bit disappointing to me, given how many other options there were.)