Well at first it's just mentioned in the opening crawl, which is then helped in the scene on the trade federation ship when Obi-Wan says "Master Yoda said I should be mindful of the future" and Qui-Gon disregards this as Obi-Wan's new master by saying "Be mindful of the sense of the moment" I also recut the balcony scene at the Jedi Temple to have Obi-Wan and Qui-Gon talking about why Qui-Gon left the Order by using some of Liam Neeson's lines from the training montage in Batman Begins.

Obi-Wan rejoins the order to train Anakin at the end when Yoda makes him a Jedi Knight, Qui-Gon and Obi-Wan still have a conection to the Jedi, they just work alone like some detectives would work alone from the police.