Jar Jar entered the city with the two Jedi following him, the locals backing off and watching, waiting for the city guard to come up and deal with the intruders, but in the meantime it was good to be home. Binks and the Jedi were quickly brought to Boss Nass, though Binks thought that cuffing him up was a bit much. Boss Nass was obvious in his bad mood, and that he just wanted the Jedi gone, even with the Jedi doing the hand waving the large Gungan barely seemed to cave, and had an ominous grin when he decided to "lend" the Jedi a small craft to go though the dangerous core pathways. Jar Jar knew Boss Nass enough that he was just giving the Jedi the vulnerable craft so that the dangerous life in the treacherous pathways would eat them for dinner, an obvious set up if he ever saw one.
While Jar Jar was musing the Jedi promptly left, and Boss Naas quickly rendered judgement on Binks by throwing him into a made to order bare cell. The next few weeks were quiet for Jar Jar, the only changes were when food was served, no one to talk to, and nothing to do but try and arrange his memories revealed when he went wrong, next time he knew what to do to get the Jedi to bring him with them.
After a few weeks his cell started to shudder as the city came under attack and after uncounted minutes Jar Jar was once again back in the forest being tackled by the Jedi.