Well, seeing that there aren't much Freeware games around in the forums, I might as well tell you my favorite of them all from what I have played. it is called IJI ( i-j-i ) pronounced E-Jee. it is a game made by Daniel Remar of Remar games.

The story starts off with the Female protagonist named IJI as she watches from a window some lights and it flashed down exploding the surface of Earth. She awakes weeks after and finds out that some aliens named the Tasen had took over the planet. She wants to know why they invaded Earth and wants them to stop and leave. So, with her body equipped with nanos while holding a Nanogun (the aliens' weapon), she goes to find the head of the Tasen to reason with it. (oh, but there is more to the story than what I am saying.)

This game has many ways of playing that you wouldn't even go through just once. You have to play it multiple times as this game has a morality of playing it with killing enemies/being a pacifist and it does change the story as it progresses. It also has some great gameplay of using the weapons and a stat system with hidden abilities that you have to find out by yourself. And try to find the easter eggs in the game...

Many words can say about this game, but it is best to show you a trailer made by Ultimortal, a pun to the difficulty in the game which is also the game creators Youtube account: