The Atlantis Series
There's something I've realized over the last few years: serious games are never taken seriously, mainly because of the lack of effects/production that I have. Looking back at some of these games today, it's cringing to see such serious cinema cutscenes with story driven plotlines when it's such a simple little freeware shooter. Live and learn I suppose. Onwards to the original description!

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Project: Atlantis and The Fall of Atlantis tells the story of the underwater city, thru the eyes of a commoner. Pilot an Atlantian tank and fight thru levels of different variety thru these two games, including

-An underwater oxygen plant
-The earth's tetonic lava plates
-The belly and insides of a giant underwater sea creature
-Inside the mechanics of an enemy tank factory
-Seaweed plantations
-Enemy base raids
-And, of course, tour Atlantis itself

These two games tell its story by in-game cut scenes and data, and consists of around 10+ levels each. The download is both games together in an auto-unzip exe.

A third chapter of the game was planned but never released. No plans are made to continue this game series.