An aftertreatment systems’ sole purpose is to reduce emissions from the engine, but all the action takes place in the combustion chamber where fresh air meets diesel fuel and compression blows up the whole mixture to turn the crankshaft. That reaction (or explosion) creates byproducts like nitogren oxide, unburned hyrocarbons and soot - or particulate matter.
That’s pretty much where the aftertreatment system comes into play. An engine without an aftertreatment would expel all these by products via black smoke.