You can definitely see the organism that causes malaria. Malaria is caused by single cell parasites that live inside our cells for most of their life cycle. They are smaller than our cells (1-2 micrometers, which is 0.0000000001 of a meter), but definitely big enough to see under a microscope. They infect red blood cells during the stage of their life cycle that causes the symptoms of malaria, and we grow them inside red blood cells in the lab. We look at them down the microscope all the time to keep track of how well they are growing, and they appear as purple blobs under certain stains. You can see pictures of them on the Wikipedia page for Plasmodium falciparum, which is the specific species of malaria parasite that causes most malaria deaths.