I. have honda pilot 2016 emission control system went on at 46.000 miles
At that age and mileage it is probably covered by your warranty.
The WHOLE system? There must be 400 parts in that system and ALL of them failed all at once? I don’t think so.
What is your question?
I presume you mean the emissions system indicator is lit. Take it to a Honda dealer for a diagnosis. You may be covered under the emissions system warranty.
Make sure the gas cap isn’t loose.