you're probably the only person on the planet who knows the answer to this question (outside of the game's developers), but
how does the game end? i never managed to beat it as a kid, and i no longer have the means to go back and try again. emulating it has also been unsuccessful. i can't find any videos of any gameplay beyond the first 3/4 worlds. the only thing i found is that there's an expert difficulty mode which is unlocked after beating normal mode, where you play the stages in reverse order as a robot version of jinbe. also wondering how that plays out too, do you still fight the bosses in that mode?
Well, I think there are others that have played it, and some did win, but hardly took their time talking about it(there was a Facebook page about the game that had the brief answer to it, though), but...
If "Easy Mode" is selected, you can only go up to World D, Maple Park, and defeat its boss, Totemator, and no farther. You're only treated to a brief "End of the road" ending in it. "Normal Mode" goes all the way to World J, Cloud Garden, where you face Jinbe and defeat him, and it ends the game in victory for Kokopolo and Tatsumo's journey. That is where it ends.
"Expert Mode", on the other hand, I'm afraid there's no bosses to fight, but at the very end, it does have one more new boss fight only in it, only against the duo themselves. And given that the mode does have a different time limit that only gets tighter by going through each world because Mech-Jinbe has an unstable battery detonates if its up, especially with Scratch Meadow, where it is the mode's last world and its tight limit is 1 minute to finish each round, you're bound to face many stumbles, unless you can memorize them very well and try to be as fast as you can, even in reverse order, and mirror-flipped.
Once you do get to the game's actual last fight, which is the only original round that isn't mirror-flipped, all you have to do is to keep on Dash-Slashing Kokopolo and Tatsumo as they try to fight back, as it is that mode's goal for the robot's creator, Jinbe, to deal justice to them(which is obvious why after finishing "Normal Mode"). The thing is, regardless of how much time you spent trying to reach it or gained more time by normal means, even gaining some more by jumping up to get treats from digesting enemies from the SnapSnap Plant, you only get 1 minute for the whole fight until the robot explodes and knocks the duo out, unconscious(they do wake up shortly, though).
The little neat surprise after it is before the robot could deliver its success, the ChompChomp Plant, the giant plant seen in the fight against Jinbe, arrives, and mistook it as its creator and snatches it up in its jaws. You do, though, get to tap the money icons afterward, and by doing so, the plant will try to shake it up, but all it will do is fling out so much money within its body, which is pretty much what's been put into the robot after Jinbe invented it and some more's been collected through its run, and goes all over Kokopolo's territory. Don't know how much, but it was quite a lot, from the looks of it.
That leads to one more ending to see in finishing Expert Mode, where the duo gets to enjoy their time with the loads of golden coins they're spending, leaving Jinbe, at that moment, down and out, and getting his last dealings of scratches from them, which is where the game's story truly ends. Not to worry, the sequel shows he's gotten better and back on his tracks. He can't really stay down from that very long.
I, of course, would've enjoyed a good boss rush mode in the game, but the DSiWare's tight size limits for its games pretty much bars it there. Too bad the 3DS port didn't have it added as a new unlockable bonus, either, but, not by beating "Expert Mode", that would be a bit frustrating. Sure, we do have Time Attack, but that's not the point.
I would've enjoyed beating the bosses back-to-back, but would also enjoy a new treat after finishing that mode under a required fast time. I was thinking more of a "Where are they now?" montage moment for all the defeated bosses that showcases what they're doing now after their defeats. My guess, other than trying to recover from their wounds, judging from the damage they received by the many harsh scratches/self-harming inflictions they took in their battles, many of them taking many different hobbies and choices in their lives.
Well, that's your answer. Hope it helps. Sorry if emulating that game was rough for you, by the way, but don't give up trying. Takes some well-adjusting, but its not impossible. And, more people should have made more videos of it past those 3/4 worlds, too. If only they took the time doing it.