2006 Honda Civic - smells like mouse waste

I had a mouse in my car which left feces and pee and it is a very horrible smell where does it get in the car and how does one get rid of the horrible smell

Suggest to focus on that part of the problem first. Any opening the size of a quarter or larger, mouse can get through. Parked w/ window left even slightly open, door ajar, sun-roofs, are the first suspects. Ask shop to put car on lift to see if there are any openings on the underside. Part of a car’s ventilation system (HVAC) is an outlet for air that comes in through vents under the windshield, often located in the rear wheel/fender area. So ask shop to double check that area.

Next step, why is mouse interested in your car? Seeking food is the most likely reason. Mouse uses sense of smell to locate food. So remove/clean all food-related stuff from car.

Once mouse can’t get in, then its time to consider cleaning & odor removing projects. Pet stores have these sorts of products.