Historical accounts of the work of J. J. Thomson find a contradiction in his work. On the one hand, he is presented as a Maxwellian theoretical physicist dealing with a typically Victorian entity, the ether. On the other hand, the analysis of his experimental work at the Cavendish seems to have little connection with his mathematical work. In this paper, I discuss the metaphysical views of J. J. Thomson, and argue that his deep belief in the ultimate continuity of matter (...) can be seen to give a framework to both his theoretical and his experimental work. His metaphysical beliefs were not in the least shaken by the discovery of discrete phenomena and entities, not even by his suggestion of the existence of corpuscles later known as electrons. His formation in Cambridge, together with some ideas that he acquired in his youth at Owens College, Manchester, are the key to understanding his metaphysics and the role it plays in his scientific work. (shrink)