Okay...I've actually done a lot of thinking about this.
First I'd start with no Qui-gon. His character is pointless.
Episode I starts with Obi-wan and his apprentice protecting the Queen of Naboo (a sixteen year old woman who inherited from her father) from invading Mandalorian forces during the Clone Wars.
The Mandalorians have been cloning themselves to make their army larger in a short amount of time. Their leader is Jango Fett and his biological heir is Boba. They try get her to Coruscant, where she will be protected by the Jedi Order. Their ship is hit to hard by Mandalorian fire and the are forced to land in the near by Tatoo system. There they meet a young orphan named Anakin (16 years old in this version) who tells them he can fix their ship if they promise to take him with him. We later learn he wasn't an orphan, but ran away from home because of an abusive stepfather. Obi-wan senses the force in Anakin, and promises that he will take him before the council. During this time, Anakin and Obi-wan's apprentice become good friends, and there is flirtation between him and the Queen.
They get to Coruscant, where Chancellor Palapatine promises a full armada to put down this Mandalorian Threat. The council tells Obi-wan that Anakin is too old (this time he is), but Anakin proves he is not. Mace Windu and a small force of Jedi head back to Naboo with the armada.
They head back, and a huge battle begins.
On the surface, Obi-wan, His Apprentice and Anakin are ambushed by Darth Maul. The Queen, Mace and the jedi attempt to free the throne. The apprentice is killed and Maul now goes after Anakin. But Anakin proves himself to be a formidable Lightsaber fighter. Maul is not killed, however, because he is called back home by his master.
The fight on Naboo is over, The Republic wins. Mace slays Jango Fett, making young Boba swear vengeance for his father.
Episode II-4 years pass, The Mandalorians have not been seen since the battle of Naboo. Anakin has become strong in the force and has married the Queen of Naboo. In this version, love and marriage is allowed, just like it is in the Star Wars books that take place after Episode VI. Palpatine's time as Chancellor is coming to an end, but he does not want to give it up. As Dark Lord of the Sith, he conspires with the Mandalorians, giving them better cloning tech and equipment. The queen of Naboo tells Anakin she is pregnant with twins. Anakin is happy, his life could not be better, til the day Palpatine calls him to his office. Palpatine has become close friends with the young man. Palpatine tells him his plans to take absolute power, and that he wants to share it with him. As a war fleet of Mandalorian ships appears in the skies of Coruscant, Darth Maul enters the office. Palpatine knows that Anakin would want vengeance against Maul for killing his friend, and he uses that to his advantage. Anakin and Maul duel, as the Jedi temple is attacked. A chase scene begins, with Boba Fett (in the Slave I) chasing Mace Windu in the skylanes of Coruscant. Maul is defeated, and Anakin falls deeper to the dark side. Palpatine promises that Anakin will be his second in command, and can change the problems in the universe. He will give him power to protect his family from the Mandalorian invaders. Anakin agrees, and becomes his apprentice. But he must defeat the traitor in the Jedi Council, Mace Windu.
Mace reaches the offices of the Chancellor. Boba Fett shoots him in the chest, not a killing wound, but enough to bring him to his knees. As Boba Fett puts the gun against his head, Anakin barges out screaming "Traitor!!!" and cuts off Mace's head. Boba Fett blast away to safety. Palpatine tells him of another traitor, his master. A space chase begins, between Obi-wan and Anakin. Anakin is sthe superior, shooting Obi-wan down above the skies of Mustafar, a nearby planet made of molten material.
Obi-wan crashes, but gets out before his ship lands in the lava.
On the solid ground, the duel begins. Anakin, clouded by the dark side, accuses his master of treason. Obi-wan tells him that he's being manipulated.
Anakin, being too proud to admit he is being fooled, starts the fight.
The duel is pretty much the same. The end is different. His limbs are burned off, not cut. He is burned to his waist, and his hands are burned off. Obi-wan uses the force to pull him out of the lava, but leaves on Mustafar. He feels too much grief and failure to bring him back. He heads toward the Queen on Coruscant to tell her the news. At this time, Palpatine declares himself Emperor. The Mandalorian attack ends as Boba Fett gives over his power the Palpatine. Obi-wan knows that the children of Anakin would never be safe on Coruscant, so he takes what remain of the order (Yoda and a few others) and they leave to find refuge elsewhere and find the surviving Jedi.
Palpatine saves Anakin, and assumes Obi-wan died. Darth Vader is created. Palpatine's suspicions about Obi-wan are false, and the hunt to exterminate the Jedi begins.
Episode III- The Queen has given birth to Luke and Leia. Darth Vader hunts for his wife and former master.
The film takes place over many worlds. The Rebel Alliance begins.
It all culminates in a final huge space battle between the Jedi and Rebels Vs. the Empire. Darth Vader knows which ship his wife is in, and he hunts it down.
In the final moments, The Queen says her farewells to her children, Obi-wan and Bail Organa. Obi-wan promises to take Luke to his step-uncle and Bail agrees to raise Leia. Yoda tells them he will hide himself away, to be the last jedi trainer. She knows the only way for Vader to stop his pursuit is to assume that she, the twins, and Obi-wan are dead. The Queen tricks them, and stays on board. We see a look between Obi-wan and her. He understands why she stays back. The children and their protectors leave on escape pods as the Queen heads the frigate she is on toward the bridge of a Star Destroyer. As it explodes, Vader screams and begins to shoot down ships in rage. He doesn't care who they are.
The film ends the same way Episode III did, we see Vader, Palptine and Tarkin (who has a much larger role in the film) look on as the Death Star is constructed.
I know it needs work, but of course it would be revised and I left out stuff i thought because I'm getting tired of typing.