As Qui-Gon Jinn made his decision about training Anakin, Obi-Wan warns Qui-Gon to not defy the Jedi Council again.

From the script:

OBI-WAN : The boy will not pass the Council's tests, Master, and you know it. He is far too old.

QUI-GON : Anakin will become A Jedi...I promise you.

OBI-WAN : Don't defy the Council, Master..not again.

QUI-GON : I will do what I must.


QUI-GON : You still have much to learn, my young apprentice.

What did Obi-Wan mean by that statement? Is this a reference to the expanded universe?

10. Wrote shocking tell-all book, 'Behind the Council, Secrets Revealed'.
9. Told Council answer to Prophecy was: '42'
8. Refused to get a haircut.
7. Fly fishing in Yoda's dinner.
6. Insisted on keeping 'pathetic life forms'.
5. Insisted on wearing kilt instead of pants.
4. When they got their lightsaber shipment he took the only green one.
3. Introduced an entire class of initiates to the art of Force food fighting.
2. Skinny dipping in the Temple garden fountain.
1. Played 'Short People' and 'It's Not Easy Being Green' at Yoda's Birthday Celebration.

(from the now-defunct qui-gonline.org: "Jedi Top 10 Lists", Internet Archive)

On a more serious note:

"I break the rules not because it suits me, but because sometimes during a mission the rules get in the way."
- Qui-Gon Jinn to a young Obi-Wan Kenobi (Jedi Apprentice: The Defenders of the Dead)

  • Refused Council's suggestion to take a Padawan before Telos IV journey

  • Brought Xanatos to the Jedi Temple for training, despite the fact that the child was older than the accepted age for training {someone seems to be in a pattern here} (Jedi — The Dark Side series)

  • He also defied the Council order not to involve Obi-Wan in investigation of sabotage at the Jedi Temple in Jedi Apprentice series:

    In that instant, Qui-Gon made a decision. He was not allowed to involve Obi-Wan in the investigation.
    But things had changed. He turned and acknowledged Obi-Wan for the first time. "I need your help," he said.
    Obi-Wan stood frozen, surprised at Qui-Gon's words.
    "I need to see Tahl and report all this," Qui-Gon said. "I'd like you to come along."
    "But the Council--”
    "It is my investigation," Qui-Gon said firmly. "You have faced Xanatos before. You could be helpful. So come." (Star Wars: Jedi Apprentice #7 - The Captive Temple)

  • And later on, in the same book, he defied the council again (by choosing to go after Xanatos, despite council's disapproval. But the council explicitly did NOT forbid him to do that, in all fairness).

    "I do not understand your hesitation," Qui-Gon said. "Xanatos is a powerful enemy of the Jedi."
    "Enemy of yours, I think he is," Yoda said, his gray-blue eyes intent on Qui-Gon. "Fruitless, a search may be. Wasted energy, it is. And too much anger I sense in you, Qui-Gon. Xanatos will reappear. Meet him you shall. But seek it you shall not."
    "We do not forbid you," Mace Windu said. "But know that if you do, you go without our support."
    Qui-Gon did not react. He bowed stiffly and turned on his heel. Obi-Wan followed him from the room.
    "Not this time," Qui-Gon said grimly. "I am going after him, Obi-Wan."
    Surprised, Obi-Wan fell silent. He knew how much Qui-Gon respected the wishes of the Council. To oppose them must be a wrenching decision.

  • Developed a personal relationship with Tahl

  • Went to New Apsolon (against the orders of the Council) to discover what may have happened to Tahl. This resulted in his almost succumbing to the Dark side when she died. (Jedi Apprentice #14: The Ties That Bind):

    Mace Windu pointed his finger at Qui-Gon. "Know this, Qui-Gon Jinn. If you leave to find Tahl, you do it against our wishes and direction."
    It was the strongest condemnation Mace Windu could give, short of forbidding it. Qui-Gon nodded curtly. He turned and left the chamber, feeling Obi-Wan at his heels.

  • I think there was at least one more major instance, durnig The Stark Hyperspace War, but couldn't find details yet.

  • Also, in Stark Hyperspace War, Vos and his Master Tholme discuss how Qui-Gon is basically a hippie (doesn't take baths and smells and dresses shabbily). The impression one gets is that this is out of norm for a Jedi.

Is this a reference to the expanded universe?

No, it is not.

George Lucas is on record as not acknowledging the EU's existence even if he incorporated some minor details from it such as Coruscant.

However, it's quite possible that there was a marching order to EU writers to include "Qui-Gon being rebellious" into their works, most likely by virtue of embedding that characteristic as a major point in Holocron database which all EU authors must consult before working on licensed properties.

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    THIS. Well, the more serious part, anyway. Qui-Gon was quite known in the Expanded Universe for doing his own thing despite the Council's wishes. – Omegacron Sep 24 '14 at 15:17
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    What are the rules to play 'It's Not Easy Being Green'? Is it a table-top game? So many questions! (And yes, I upvoted for the first part of the answer.) – bitmask Sep 24 '14 at 18:33
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    Everybody was Force-food-fighting...those cats were fast as lightning. – Chris B. Behrens Sep 24 '14 at 21:13
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    Crud, 42 upvotes, now I can't upvote... – Unsigned Sep 25 '14 at 19:52

AFAIK it is never explained, but considering that Liam Neeson described his character as

"a bit of a loner, and a bit of a slight maverick"

to MovieTalk, it seems logical that they've clashed before. Apparently in the novel it is said that Qui-Gon has failed to follow all the rules all the time, which is the reason he was passed over for a seat on the Jedi Council when he was otherwise qualified.

There seems to be an example of a 13-year-old Qui-Gon defying the Council in Jedi Apprentice #7, The Captive Temple, by Jude Watson, apparently.

  • @Quincunx I was going to upvote this, then noticed.. couldnt be the one that changed it. ;) – paqogomez Sep 25 '14 at 7:23
  • @ DVK: I haven't read the story, I went by a description I saw somewhere. However, I now notice that there's another Jedi Apprentice story that seems appropriate: Jedi Apprentice #14, "The Ties That Bind", by Jude Watson: "In this tale, Qui-Gon Jinn and Obi-Wan Kenobi defy the Jedi Council. They are out to help an old friend who is in trouble. Will their allegiance to the Jedi be their ultimate test in this adventure?" – BCdotWEB Sep 25 '14 at 7:53

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