Sometimes bacteria multiply so rapidly that they crowd out host tissues and disrupt normal function. Sometimes they kill cells and tissues outright. Sometimes they make toxins that can paralyze, destroy cells' metabolic machinery, or precipitate a massive immune reaction that is itself toxic.
In general, your body fights disease by keeping things out of your body that is foreign. Your primary defense against pathogenic germs is physical barriers like your skin. You also produce pathogen-destroying chemicals, like lysozyme, found on parts of your body without skin, including your tears and mucus membranes.