The disclosed invention includes apparatus and methods that may be used for plasma-based deposition of thin layers of material on separate or continuous web substrates at very low temperatures with very low defect density. It achieves superior control of gas phase chemistry by controlling the sequence of introduction of gaseous components. It also has substantially independent control over the rate of chemical processes in the gas and of the amount of power and energy of ion bombardment. Such control enables high quality single and multi-layer films to be deposited cost effectively and uniformly over larger areas under very low temperature conditions.