Currently, peptic ulcers are widely considered an infectious disease caused by Helicobacter pylori due to 3 supporting evidences, and this etiology may explain 3 other observations. However, it cannot withstand the challenges of all the 15 major characteristics and the other 75 observations/phenomena of peptic ulcers. To address these challenges, a recently published Complex Causal Relationship with its accompanying methodologies was applied to analyze the existing data. Peptic ulcers are identified as a psychosomatic disease triggered by psychological stress, where Helicobacter pylori plays a secondary role in the late phase of ulceration. This new etiology addresses all the characteristics, observations/phenomena, controversies, and mysteries of peptic ulcers in a series of 6 articles. This sixth article focuses on the controversies associated with Helicobacter pylori. In-depth analyses find that all the 3 supporting evidences are illusions, and all the 3 explainable observations are misinterpreted, indicating that none of the 15 characteristics and 81 observations/phenomena of peptic ulcers can be elucidated by the etiology based on Helicobacter pylori. Moreover, the definitions of ‘etiological factor’, controversies on H. pylori, epidemiological studies, characteristics of the disease, and historical observations suggest ‘peptic ulcers are an infectious disease caused by Helicobacter pylori’ is an illusion and thus, the African enigma, a mystery derived from the illusion, does not exist. Similar illusions widely exist in medical research, resulting in direct interference with the true understanding of diseases. A full understanding of the pathogenesis of peptic ulcers highlights the guiding role of philosophy in life science and medical research.