What remains in the body after an immune battle?
Your body has different ways to act, depending on the type of pathogen.
Many extracellular pathogens get attacked by antibodies, witch stick to the surface of the pathogen and can prevent the uptake of nutrients or from attaching to cells of your body. In many cases these antibodies also facilitate the uptake of pathogens by macrophages, who will digest them. In both cases the pathogen will die and thus be inactivated. The remains can be broken down in your body to serve as nutrients just as any type of food would.
Intracelluar pathogens are removed by killing the cells that host them. This happens by inducing cell lysis in these cells through the formation of pores in the cell membrane or interactions with Natural Killer Cells. The host cells will die and the pathogen will not be able to replicate, the celldebris is broken down to its building blocks (amino acides, nucleic acids e.d.) and recycled by the body.