Oh man.
This is Prisoners of the Lost Universe, a 1983 fantasy sci-fi film starring the original Battlestar Galatica's Apollo as Dan (a guy with a kendo stick), a few other generally unremarkable people, and Peter O'Farrell playing essentially his exact same character from Hawk the Slayer.
Dan and local TV reporter Carrie get into a car accident and shortly thereafter end up in a parallel dimension. Alternate universe. Whatever. Frankly, the Rifftrax summary linked above explains the plot far better than I ever could.
However, it suffices to say that Dan and Carrie almost immediately meet "The Green Man" (or, if you believe IMDB, "Greenman"), a very green (grey?) elf wielding a crude rifle powered by compressed air. At approximately the 24 minute mark, Green Man saves Dan and Carrie from some unfriendly wildlife (a "water beast") with a crude-looking compressed air rifle, and Dan immediately realizes that "these [native fruit] pods are full of some kind of gas".
Every single point of your description matches:
"The guy could have been away from Earth for a long time before returning, like an astronaut."
There's a time differential between Earth and this alternate universe. Dr. Hartmann, the inventor of the teleporter, steps into the machine only minutes before Carrie, yet she arrives years after. Dan steps in seconds after Carrie but arrives days/weeks after she arrives.
"The thing I remember the most is one of the guys picked a round fruit to use as the propulsion for a weapon, like it was full of compressed air. Don't remember much else. The guy could have been some sort of guide or maybe local."
One hundred percent straight from the movie and scene I just described.
"The weapon if I recall correctly looks similar to a rifle and I think it shot a metal rod."
Exact match.
"Group of 4 people maybe, and in a desert-type terrain."
Exact match. Shortly after the gas-fruit-powered-rifle scene, Carrie is kidnapped by the bad guy, Kleel. Dan meets up with The Green Man and Malachi, adventure across desert-ish terrain, meet up with a giant named "Kahar" (who strangely doesn't seem to be credited on IMDB by that name) and adventure across more desert-ish terrain on their way to rescue Carrie from Kleel's stronghold.
Live action, was not a cartoon.
Yes, indeed.
Please, grab your kendo stick and tell me I have correctly identified your movie! :D