Inside the Jedi Council chamber, Qui-Gon gives his report including the attack by a Sith Lord. This unsettles the room and they decide that Qui-Gon and Obi-Wan should remain with the Queen for the time being. Before he leaves, however, he tells them of Anakin and his miracle birth. The Council is stunned and Master Mace Windu suggests that Qui-Gon believes that Anakin is the prophesized Chosen One that will bring balance to the Force. Qui-Gon presses and they agree to test the boy.

In the Senate Chamber, the Queen pleads her case, but when the Trade Federation demands an investigation, the Chancellor concedes. Dismayed by the politics being played, she calls for a vote of “no confidence”.
Anakin busts into the Queen’s chamber looking for Padme, but only the Queen is there. He tells her that he is going to be tested as a Jedi and she wishes him well.

As Obi-Wan and Qui-Gon await the Council’s decision, Obi-Wan wonders why his master continues to defy the Council and not follow the Jedi Code as closely as he should. He knows that no one is allowed to be trained after the age of one and Anakin is nine. Qui-Gon says Anakin will be trained as a Jedi, and they he only pushes what he knows to be right in the living Force.

Anakin faces the Jedi Masters and handles their basic mind tests easily. He admits to missing his mother and Yoda tells him that this attachment is a grave concern for them. He must let go of his fear of loss.

In her quarters, Jar Jar tells the Queen that the Gungans won’t go down easily and that they have a grand army. They are interrupted by the return of Palpatine who has been nominated to succeed Valorum. The Queen is unimpressed and decides, against their advice, to return to Naboo.

The Council tells Qui-Gon that Anakin will not be trained. He has too much anger in him already. Qui-Gon is incensed by this and says he will take Anakin on as his Padawan! Obi-Wan is shocked, and Qui-Gon follows by saying the Obi-Wan is ready for the Jedi Trials. Yoda and Mace are not convinced and decide to send them all to Naboo with the Queen. Anakin’s fate will have to wait. As they leave it is clear that a rift has formed between Qui-Gon and Obi-Wan.
Sidious contacts Nute Gunray on Naboo and learns that the planet is secure. Sidious says the Senate will not intercede, but Darth Maul will be joining them to handle the Jedi.

On their return trip to Naboo, Qui-Gon is still upset by the Council’s rejection, but he tries to move past it. They all question the Queen’s intentions upon returning to her planet. She calls on Jar Jar for help.

On the surface, they wait for Jar Jar’s return from the underwater city. Anakin tells Padme of the Council’s decision. She tells him not to give up and that even the Queen changes her mind. She is now planning to attack the Trade Federation!
The two Jedi still are not speaking to each other. Obi-Wan decides he doesn’t want to throw away twenty years of history over this. He knows that Qui-Gon has never been more passionate about anything. The two men talk and Qui-Gon reiterates his belief that Obi-Wan will be a great Jedi. The two men shake hands.

Jar Jar returns and says that the Gungan city is empty, but he knows where they have gone. When they arrive at the Gungan sacred place, Boss Nass is not pleased to see them. As the Queen speaks, Padme steps forward and reveals that in fact she is the Queen! Her handmaiden Sabe has been acting as a decoy! She bows before them and begs them to help. Boss Nass is pleased by this and agrees.

Impressed that Jar Jar helped bring the Gungans and Naboo together, Nass promotes Jar Jar to a general. Scouts return and bring leaders of the Naboo underground resistance. The plan is for the Gungan army to fight the main battle, while the Queen and the Jedi sneak into the Palace to capture the Viceroy and Naboo fighters try to knock out the droid control ship in orbit.

Inside the Palace, Gunray tells Sidious of the army massing nearby, and Sidious gives him the go ahead to wipe all of them out.

As the battle begins, Anakin is glad that Qui-Gon and Obi-Wan have made up as he did not want to come between them. He and Padme talk briefly about their feelings for each other.

Outside the Gungan shields are holding off the heavy fire, but the battle droids are able to make it through and the Battle of Naboo begins in earnest.

Nute and the other leaders are fearful upon learning that the Jedi have breached the Palace. Maul says not to worry and goes off to meet them.