Methods for treating systemic disease in oral biofilms having a facultative anaerobic bacteria pathogen present including providing a periodontal medicament delivery tray having a seal against a patient's adjacent gums containing the oral biofilms with the systemic disease, said seal formed so as to have no contact with teeth, applying to the gingival tissue (sulcus or periodontal pocket) a biofilm penetrating antimicrobial agent, removing the imbedded anaerobic bacteria from the gingival tissue following at least one applying of the antimicrobial agent to the gingival tissue; repeatedly administering colloidal hydrogen peroxide gel to the gingival tissue following the removing of imbedded anaerobic bacteria; and following each administering cleaning the gingival tissue with a cleaning agent directly following the administering of the colloidal hydrogen peroxide gel for modifying the environment from anaerobic to aerobic.