There are 2 versions of Prime Directive d20, one based on the D&D 3.5 PHB and the other based on D20 Modern. Are there any noteworthy differences between the two versions, or did they just make a second version of it for people who had d20 Modern but not D&D?
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As the other answer states, d20Modern and D20 are different systems entirely, albeit with some similarities.
If memory serves, d20Modern is built on the concept of the same six stats, but your 1st 3 levels are basically just a basic class specialized for one of the skills. You then have advanced classes that give special feats and abilities as you progress in them. The d20Future book added a lot of sci-fi tech and the idea of technology levels.
I won't cover all of the ins and outs of d20, as I'm assuming it's ubiquitous enough to not need a lot explanation. But it's definitely different from d20Modern.