Unity 2D respawning Instantiate issue

I am making a 2D Space-invaders style game and am having GREAT difficulty with respawning. What i want to happen is when the SpaceShip is hit, it gets Destroyed, e.x. Destroy();

But when i try to Instantiate() the Prefab of the SpaceShip it does the (clone)(clone) problem, so I am trying to Make an Empty GameObject run script that spawns in a Prefab of the SpaceShip, AND when it gets Destroy(); it respawns after 3 seconds. Much help appreciated, and i'm coding in JavaScript.