You can use a Raycast through the mouse position to find out what 3D geometry the mouse pointer is over, and then create your projectile at your player's location, heading toward that point. e.g.

var ray = Camera.main.ScreenPointToRay (Input.mousePosition);
var hit : RaycastHit;
if (Physics.Raycast (ray, hit, 100)) 
{
  // Get your player object's position (could be any way, this is just one possible way)
  var playerT = GameObject.FindWithTag("Player").transform;
  // Now you have where your player is and a 3D point the mouse is over
  Debug.DrawLine (playerT.position, hit.point);
}

for more info: you can get the direction of mouse pos and middle of the screen vector using Vector2 class methods. also if you want to know what point in 3d space mouse is on, then you can use camera.ScreenToWorldPoint as z argument you should get the distance from the camera that you want x,y to be calculated. then you can use that point to look at it and place a target object in the position of the mouse if needed. i think in your game you just need to get the direction between mouse position and center of the screen and then use that direction for (y axis rotation of your player) see the evac city tutorial for an example