Alter Echo takes place on Proteus, a planet whose entire surface is covered by an organic substance called Multiplast. ("Plast for short.) Multiplast is the most important substance in the Universe because rare individuals called Shapers can physically shape it into all sorts of bio-machines.
You play Nevin, a Shaper who works for one of the many Corporations that mine Multiplast. You're not just any Shaper you can also Time Dilate, something most Shapers can't do. (Your ability to merge with the energy fields of Multiplast is so powerful that you can effectively stop time. Useful in combat, obviously.)
Your employers have sent you to Proteus because a Shaper named Paavo has created a new form of Plast and it's gotten out of control. The new Plast (called Xenoplast) has become self-aware. It knows that humanity plans to exploit it and it doesn't want to suffer that fate. To make matters worse, it's figured out a way to retaliate.
The Xenoplast manufactures enemies to fight you much like our bodies produce anti-bodies to fight infection. These opponents take the form of various combat drones, and later in the game, clones of people you know. It's a long, hard fight ahead of you, and you'll have to call upon every ounce of skill and courage you've got. The last thing you wanted was to have to save humanity, but hey if you don't do it, no one else will.