Because it was originally planned to be a CD release in collaboration with Sony and a much larger game, but that fell through so they chopped it down to what could fit on a cartridge and the rest got recycled over to Chrono Trigger. To recoup the excess development costs they raised the price.
There's plenty of datamined stuff that was never used, as well as photographs from magazines and locations on the map you can't explore.
This is a list of all the unused or dummied content within each versions of Secret of Mana. Barring glitches or cheat codes, it's impossible to get the sword up to Level 9, unlike every other weapon. However, if you do get an extra Sword Orb by whatever means, it can be upgraded, and comes...
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Unknown Areas from Secret of Mana’s cut content February 28, 2021 Interest has abounded for content deleted from Secret of…
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Oh man, Secret of Mana (and the cut content) is totally my jam. I spent hours and hours a few years ago studying this particular subject, cross-referencing Secret of Mana areas with Chrono Trigger areas, etc. I eventually concluded that Secret of Mana was originally supposed to contain time travel, which is why there are occasional things that are completely out of place, like the subway system area during the third-to-last dungeon. I also think Xenogears was supposed to be Chrono Trigger 2, and that's why it has so many little CT elements (all right near the beginning of the game) including
an actual appearance by Lucca. Xenogears takes place over four distinct time periods (though only one is playable and the rest are shown in flashbacks of the reincarnated protagonists) and I get the strong vibe that it started life as a time-travel game where you actually went to these other distinct time periods. One of them is even an advanced civilization from the past that sank into the ocean, just like in CT.
With CT and SoM I scrounged up a lot of little things like:
-On the overworld map in The Empire (SoM) you can clearly see what looks like a fairground, with a town fair and a carousel, but you can't go there in the actual explorable town it's next to. CT opens with the Milennial Fair, which bears a striking resemblance to the phantom fairground in SoM.
-Out of the four main elements, the only one that didn't get a Gigas boss in SoM was earth element. One of CT's biggest and most memorable bosses? Giga Gaia, literally Earth Giant.
-Same goes for the dragons. SoM is missing an Earth Dragon, likely because it would have been ground-based and had a different model that they didn't have time/space to make. CT has the Black Tyrano which is pretty much an Earth Dragon in every regard. This one's a bit of a reach but it makes sense combined with the Giga Gaia thing.
The list goes on and on, actually. I'm really curious what the full CD-based 32-bit Secret of Mana would have looked like. Probably some sort of combination of Chrono Trigger and Seiken Densetsu 3, which each took various elements of CT and extrapolated them out to their logical conclusions (like the elemental palaces).
Most of the cut content of SoM (which was evidently around 40% of the story) likely took place in The Empire. While I think the time travel element of SoM was abandoned fairly early, I think they got pretty far in development with what we ultimately got before they did most of the cuts. Anything pertaining to The Empire - the towns, the fortresses, the villains especially - comes off as completely slashed. In the final areas the game acts like we're supposed to know who the hell people like Fanha and Sheex are, like they had entire storylines that just got left out. The Emperor himself is also a total enigma, dies offscreen and seems rushed as hell.
Final Fantasy 15, incidentally, had a lot of the same issues (massive cuts to the world) and does
the same thing with the bad guys. The Emperor even dies offscreen with no fanfare there too, you never really get to explore the actual Empire after all the hype (or at least you get a super limited, cut-down version of it, like SoM).
While I'm on the subject of SoM, I feel like Elden Ring's designers definitely liked the game. The very end of the game in particular has huge SoM similarities, like the suddenly red sky, the ancient capitol completely transforming in layout, the great tree being in flames, and an ancient flying fortress being the final dungeon.