Godzilla arrives in Tokyo during the semi-final level and he is given two choices. Either go straight for Mecha King Ghidorah in an attempt to save Tokyo, or go around Tokyo and gather the SUPER cells so that Godzilla can transform into SUPER Godzilla, a bigger, tougher more powerful version of Godzilla that I kid you not can even do a Falcon Punch. ... really.
If Godzilla DOES become SUPER Godzilla, he can SMOKE Mecha King Ghidorah with no trouble. If he doesn't, it's a hard battle. REGARDLESS of what happens, The final stage kicks in and the aliens that have been attacking Earth the entire time bring out this big monster named Bagan who is so big Godzilla only comes up to his pecs. Bagan is so powerful he pretty much decimates Tokyo just by waking up. Now here's where the "fun" part comes. If you chose to become Super Godzilla in the previous stage, the Super transformation has worn off and you have to hold your own against this super monstrosity until the ship gets back with more Super cells to make Godzilla become SUPER Godzilla. During that time, get used to pertnear all your attacks barely doing ANYTHING to Bagan. And even WHEN Godzilla goes SUPER, Bagan is STILL bigger than him and it's STILL an uphill battle. An INCREDIBLY DIFFICULT ONE. Now, if you DIDN'T choose to become SUPER in the previous stage... well, let's just say I've never seen anyone do it. It's been described as nearly impossible to win if you don't go Super, and the worst part is, as mentioned before, even if you DO go Super, it's still incredibly difficult.
Regardless, the whole thing is accompanied by cool SNES music, aka one of the most catchiest final boss music... the perfect music to get whooped to by a guy bigger than Godzilla.
http://www.youtube.com/watch?v=RsskyUFS_oE
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After that, I declared that no final boss will ever pose a real challenge to me ever again... and so far, I've been right.