What could inflamed joints and lesions all over body mean?

Infection or more. Ghonorrhea can do this, allergies, rheumatoid arthritis. See a doctor soon. Just because it goes away it does not mean that the problem is gone it could just be deaper in your body and cause more serious problems.
Systemic problem. When your entire joint inflamed it mean you have problem in the system, like lupus, rheumatoid arthritis or other, please check with your dr.