So,  you have chosen the path of a Jedi?  Wise decision, young Padawan....  Here is an example of a story line that could develop for your character.

    While at the temple, you search for other survivors of the Sith attack.  You find quite a few, but they are too busy recovering to join your party.  In the Archives  you meet Yassari, a young Jedi Knight who has just captured a Sith Apprentice.  While questioning the prisoner, you learn there are almost as many Sith as there are Jedi.  They have been in hiding since the complete destruction of the Trayus Academy on Malachor V.  A new fearsome leader, Darth Missidus, has harnessed the ghost of Marka Ragnos,  and taken control of the scattered Sith.  Darth Missidus is a descendant of the powerful Freedon Nadd.  In his quest to destroy all Jedi, for good, Missidus is searching for the famed holocron of Adjunta Pall.  This holocron, said to hold the secrets of Pall's legendary lightsaber techniques, disappeared long ago.  With it's knowledge, Missidus believes he can crush the fledgling Jedi Resurrection and restore the Sith Empire to it's former glory.

    With your use of persuade,  you learn the Sith have a major stronghold, from which they coordinate their movements.  You take advantage of the training some of the Jedi at the temple have to offer, further guiding you on your path to destiny.  When you are ready to depart in search of the Sith base, three Jedi Knights and Master U'tari volunteer to join you.  Choose two Knights, and leave one to help defend the temple against any other attacks.  From here, you can travel to six different planets- Telos, Ossus, Firro, Deneba, Korriban, and Dantooine.

    About to leave the temple, you stop and realize: you are a Jedi now.  Sure, blasters and vibroswords are nice and all, but you need a lightsaber- it is the hallmark of a Jedi, not to mention they are "more precise than those crude blasters.  A more elegant weapon, for a more civilized time." (Thanks, 'Ben'.)  A Jedi armory is in the temple, and you decide to craft your Jedi tool.  Using parts from your brother's lightsaber, you create your custom blade (you can choose from hilt designs, single hilt, dual bladed, and blade color.  You can use a workbench to add upgrades later..)  Now that you have a blade, you need some focusing crystals to inflict more damage on your enemies - all in the name of good, of course.  The temple has none left, but you remember Dantooine has a plethora of them.  It's off to where this all began!

    When you get to Dantooine you discover the entrance to Crystal Cave has been sealed by the Sith during the invasion.  You will need some sort of blasting or drilling equipment.  The only place that comes to mind on how to get your hands on some is Firro.  You know a dealer in the Pazzak bar located in the planet's capitol city, Antium.  You and your companions head to Firro, looking for the equipment. 

   The surface of Firro is crowded and bustling with life.  This is a gambling magnet for the entire sector, and it shows.  (by the way, there will be three merchants you can buy goods from, as well as people who can tell you how to find your friend Krax the dealer, a Duros.)  You make your way to the bar and meet up with Krax.  You ask about the equipment, but he tells you it was stolen by Tebb the Hutt,  who also kidnapped Krax's wife, Leotra.  He gives you the codes to enter the Hutt's safe house, and offers you a reward (10,000 credits) if you can rescue his wife.  Reluctantly, you accept.

    Tebb's safe house proves to be a bit of a challenge, as his goons don't take lightly to Jedi- or people stealing back what was stolen, for that matter.  You find Leotra and tell her to go back to Krax.  Making your way to Tebb's audience chamber, you stumble over  a small storage room which has a piece of the famed holocron you were seeking to keep away from Missidus.  You've finally gotten to Tebb's chamber,  where you are surrounded by five assassin droids.  After you try to talk to Tebb about the equipment, he decides he really doesn't like you, and orders the droids to attack.  After you destroy them, you recover codes to a vault in Tebb's chamber, which has the equipment you seek.  With equipment in hand,  you stop by Krax's bar to collect the reward, after which you use to buy a few goods from the merchants.  Krax also informs you that Tebb was rumored to be working for an unknown dark Jedi living on Deneba.

   All right, back to Dantooine.  You drill your way through the entrance and find some interesting crystals.  In particular, you've found a crystal that responds to you.  When you remove it, a vision grips you.  It is of the exile you've never met, only heard about, doing the same thing.  Master U'tari explains to you the power of the crystal.  You also found another piece to the holocron and something else- the legendary Exile's Jedi Master Robe from before the Mandalorian Wars.  Now, you have your blade, your companions, and even a little money in your pocket.  Time to find that Sith base!

    You've made your way to Deneba, a legendary place for the Jedi.  It's surface is sparse as few inhabit this mining-heavy world.  You notice a trail leading to Mt. Meru where a small temple is located.  Once at the top, you must do battle with Sith Marauders, after which you confront the unknown Dark Jedi.  Searching his remains, you find a holo-record of a meeting between various Sith clans convening on Korriban.  After searching the temple for any useful gear you head out and prepare to may way for Korriban, the infamous planet of the Sith.

   Once on Korriban, you explore the surroundings.  It is a dead, arid planet with a cold, ghostly feeling about it.  There is a presence here.  A hunger.  Evil resides here.  For six years now, the Republic has manned a small scientific team on the planet to try and unlock some of its mysteries, yet you see no one around.  The Sith Academy is located just outside the Valley of the Dark Lords - you make your way to it.  Just outside the academy are two dead Republic soldiers.  They bear evidence a lightsaber was used to end their lives.  Inside, you are met with more Sith.  An ambush has been set for you there.  After defeating the Sith, you can enter the main hall where Darth Haden awaits.  You enter the hall and the doors close behind you, leaving you one on one with the Sith Lord.  Before you can do anything, you are forced to your knees by his Force powers.  He probes your mind, and then releases you.  "You are too strong to be a Jedi,  yet too weak to be a Sith.  You are nothing - a waste, and I will dispose of you as such."  Barely, you beat the dark lord, and discover he has a spy located on somewhere on Telos.  You check the academy for the scientists, but to no avail.  On to Telos.

    It never fails - the TSF just doesn't like new visitors it seems.  As soon as you arrive, you are placed under arrest for the murder of the Republic soldiers and scientists on Korriban.  Adm. Dol Grenn has you escorted to the holding cells.  After a while, you are released and cleared to go, but your ship has been sabotaged.  Someone has stolen the navicomputer from your ship.  You ask Grenn if he had any leads.  A holorecord shows a figure dressed in dark robes coming out of your ship.  Grenn checks the transport logs and sees only one departure within the last few hours.  It was bound for Telos - to the Jedi Academy!   Most intrigued. U'tari suggests you go down to the academy to try to locate this mysterious saboteur.  Grenn agrees, and lends you an orbital shuttle.

   When you arrive at the academy, you are greeted by Master Cypher Oldon, a member of the council at the academy.  You tell him what has happened over the last few days, and he tells you a new Padawan had just arrived.  You need to take the turbo lift to the Padawan Housing section of the academy.  You enter the lift and select the Padawan level, only to be automatically sent to a detention chamber far below the main academy.  Once there, the doors lock and you and your companions are stranded.  A few moments later, Master Oldon arrives.  You ask what is going on.  He responds: "You had the chance to join us - to become more than a mere Jedi.  Instead, you have sided against us.  You have the power to end my master, and this I cannot allow."  Master Oldon is the unknown assailant and spy on Telos!  After a rather lengthy battle, you overpower the betrayer.  "If you only knew the POWER my master can offer you.  He can teach you to harness your abilities - and, in time, you could overthrow him.  I'm giving you one last chance to join us.  Release yourself from the shackles of the Jedi."  You decide to turn him down.  "Get up Sith Lord, you will be held responsible for your betrayal," you respond.  "Very well.  Then, prepare to die, Jedi!"  Oldon forces you to kill him.  On his body you find the code to a sealed vault in the academy where your navicomputor is.   You make your way back to the hanger and take off.  Back at the station, you ask U'tari to re-install the navicomputer.  Consol intact, you are ready to head to the last planet, Ossus.

    On Ossus, you wander through the ruins of the ancient Jedi stroghold.  An old Jedi library is locate just south of where you landed, so you decide to check it out.  Inside the building you meet up with more Sith. After dispatching them you've found your way to a dark room in the library where you see a lone figure standing in the light from a holo-display.  It is the man from Dantooine- the reconstruction specialist!  He draws his lightsabers and attacks.  Using your Force powers you stun him long enough to take him down.  As you strike the final blow, a burst of energy explodes from his body.  His remains give you the final piece to the holocron, and reveal the location of the Sith base.  It is on Ganath!

   On board your vessel, you receive a message from the Jedi Knight you left back at the temple on Coruscant - the surviving Jedi have regrouped and are ready for a final assault on the Sith.  You give them the location and tell them to meet you there.

   Upon arriving at Ganath, you encounter a fleet of Sith warships.  You, along with four squadrons of Jedi fighters, must battle through the fleet and land on Ganath. (You have to man the turret)  You narrowly make it through the space battle and land.  On the surface, not only do you encounter more Sith,  you have to fend off gizkas!  Your Jedi reinforcements arrive and a major battle breaks out.  While the other Jedi are taking care of the Sith, you make your way to the obelisk to the west.  Inside, you are sealed off from the others, leaving you all alone - again.  A shadowy figure approaches.  It is Darth Missidus.  He asks you why you chose to not follow your Force abilities sooner.  Why you waited until you were forced to make a decision.  After a brief conversation, he tells you, "Now I will show you the error in your ways."  The ghosts of Freedon Nadd and Marka Ragnos appear, and attack.  You slice through them but they do not die- they are ghosts.  Your only chance for survival is to defeat Missidus.  Once he is dead, the spirits can be released and finally laid to rest.  You take down the evil Sith, but he stuns you long enough to get back up.  You deflect debris as Missidus desperately hurls it towards you.  After you take him down a second time, you are stunned again.  A second, less powerful Missidus appears.  You take care of him easily, and concentrate on the original Sith.  A third critical strike takes him down yet again.  And,  again, you are stunned.  Missidus leaves while you are unable to move.  Missidus has escaped!  after you come to, Master U'tari informs you the battle is over - the Sith are defeated.  All of them.  You tell him Missidus got away. He looks away.  "Then the Sith will return, some day- but not today...  We must concentrate our efforts now on rebuilding the Order and helping the Republic recover.  The galaxy is safe.....For now...."

    This is just a general run-through of one of the paths you can take if you decide to initially go towards the light side.  You can go to the planets in any order you choose, except Ganath - it will be the final battle between Jedi and Sith, and will crush the resurrection of one side.  Even in the final battle, you can determine which side will win.  For instance, say you are a Jedi.  If you start slicing through too many of the Jedi, the Sith will overpower them easily.  (The battle forces you to take a part if you want the Jedi to prevail)  But since this game will have a dynamic twist to it, you will probably have to battle the remaining Sith, since you sided against them earlier.  Of course, you can always make a little detour and slay some innocents, or torture your captives, etc.  There will be chances to learn new Force powers, which you can master, but will you have to practice them.  Also, "friendly fire" will be a constant.  You can slay your Jedi/Sith companions and pick up new ones at the next planet.  As you complete missions and side quests on planets, you will gain a reputation factor, which will influence dialog in your conversations. (ie if you have a reputation of being a Jedi, light sided characters will answer your questions more easily - persuade also plays a role.  Simiarly, dark-sided characters will not be so easy to get information out of.  If you have a rep of being a cruel, ruthless killer, it will be the opposite.)  Your conversations with companions will develop a rapport,  which will either open up, or close, extra dialog options.  Some civilians will be able to become party members.  And, of course, you can train them in your respective path.