There are many marvels of evolution's ability to come up with robust complex distributed systems which work way better than anything we build. The one I've learned about most recently is the https://en.wikipedia.org/wiki/Immunological_synapse in which different kinds of white blood cells gather around a bit of evidence that one of them found and decide whether to shoot the messenger (clonal anergy), or raise a clone army to defeat the invader (T-cell activation).

Imagine that it's maybe the 1800's and you're asking why somebody who has already survived smallpox is not susceptible to becoming infected again. If you offered an explanation involving tiny detectives wandering around and collecting evidence which they present to each other and decide whether to multiply... one in which the tolerance comes from the detectives from the previous fight still hanging around in your lymph nodes ready to spring into action if they run across the right kind of evidence. Well that would probably be a more complicated explanation that anybody at the time would offer, and it would also be correct.