Player instance clone to load transform from prefab

I use code to generate a clone of the prefab player. I have a "bad guy" on the stage that will follow his transform using navmesh. I made a game object drop on the badguy and I loaded the prefab but when i create it, it does not load the clones transform. No errors just simply doesnt follow the transform because its not loading the clones transform. I just don't know how to reference a clone's transform without the player prefab on stage originally which I dont want to do.