The game is inspired by the match mechanic popularized originally by Dungeon Raid (and later Puzzle Craft) where you create chains of resources, in order to gain resources/perform actions.
Puzzle Empires is about building your civilization throughout the ages. You'll research technologies all the way from fire & tool making, to genetics & cryogenics. Each technology will provide some passive benefit (+1 wood when collecting wood, for instance) or an ability that you can trigger at any time. Some technologies will allow you to unlock buildings which you can produce, such as farms and guard towers, which can influence the playfield and provide some interesting effects.
Like Dungeon Raid, Puzzle Empires is primarily an endless "see how long you can survive" type game, with a high score at the end. It will be possible to win, however, through the production of a certain end-game technology -- possibly something like the shuttle to in Civilization (not sure yet). As you're trying to survive, you'll need to balance food production -- to prevent starvation -- and military strength, to defeat invaders. Invaders appear on the screen and march down the screen at the end of each turn. If they reach your settlement, it becomes damaged. While it can be repaired, if your settlement's HP reaches 0, the game is over.

