The Future Time Travel Squadron returns to India and reunites with Baloo and Bagheera in the jungles. Although happy to see old friends again, Baloo missesMowgli, the man cub who was lured into the Man Village, and Mowgli is getting tired of life in the man village and wishes to go back into the jungle again. The FT Squad (minus Widget, Walden, Yao, Ling, Chien Po and Colonel Hathi) goes with Baloo to see Mowgli and they escape back into the jungle. However, they are unaware that their old enemy, Shere Khan, is back, this time for revenge.
During this adventure, the squadron will meet Shanti, the girl who lured Mowgli into the Man Village in the first place.
- This is the second sequel in the series. The first one is The FT Squad's Adventures in Toy Story 2, sequel toThe FT Squad's Adventures in Toy Story.
- Widget, Walden, Yao, Ling, Chien Po, and Colonel Hathi do not accompany Baloo and the other squad members when they go to get Mowgli. Widget, Walden, Yao, Ling and Chien Po stay with Bagheera, while Colonel Hathi leads his elephant patrol to keep Baloo from reaching the Man Village, which is Bagheera's "plan B." However, these six members will reunite with the others and continue going on adventures in the future.
- Kyle the Otter, the squadron's leader, doesn't stay with Bagheera because after what happened in the first movie, Kyle concluded that he and his fellow teammates could take on Shere Khan in a fight together. Baloo says one time "We've handled Old Stripes once and we'll do it again," and this is the reason why Kyle doesn't show concern with letting Mowgli back into the jungle.
- This movie will star two characters who were voiced by John Goodman; Baloo and Rex.