As a result of his work at Berkeley, Emery was invited to join the Brookhaven National Laboratory's Physics Department in 1964. After joining BNL he worked on fundamental theories for the behaviour of helium-3/helium-4 mixtures and later turned to the theory of organic conductors and superconductors. He provided insights into general many-body aspects of boson and fermion systems. Through this work, Emery became one of the world's leading theorists in the study of phase transitions, where substances change state between liquid, solid and gas.