Dodo came under the influence of WOTAN and the Doctor used hypnosis to break the control and she went to the country to rest. That's the last we saw of her, goodbye Dodo. In the meantime we are getting to know Polly (a secretary to the scientists who designed WOTAN) and Ben (a Sailor who Polly took a liking to).
The name WOTAN has some interesting connotations .. the name of a Germanic God, etc, including the Wotanism sect created by David Lane where it's an acronym meaning Will Of The Aryan Nation. Another instance of the Doctor Who writers presenting ideas related to Nazi Germany as evil.
In any case the War Machines are very capable. Army units are sent against them only to have their guns and hand grenades be rendered inoperable allowing the machine to easily kill the soldiers. However somehow the Doctor is able to stand firm as the machine approaches him and through some kind of willpower cause the machine to become docile allowing him to disarm it. He then studies it for awhile, determines there are at least 11 other machines, etc. Eventually he reprograms another captured to go to the headquarters where WOTAN is, and destroy the central computer. The centralized control system, once destroyed, renders the whole threat harmless. Won't these evil villains ever learn that centralized control systems make for a fragile plan, because all one has to do is knock out the central computer and the whole plan is dead. The Internet shows the power of decentralized control systems.
Anyway... Curiously, at the start of the latter serial, the Doctor comments that he feels the same sensation as he felt when the Daleks were around. While this appears to be intended to equate the War Machines and WOTAN to the Daleks, it is interesting to note that the events of the serial are revealed later in the series to happen contemporaneously with the Second Doctor serial The Evil of the Daleks.
The obvious theme is the evils of the coming computer age. What is the role of humans and will humans be rendered useless by the machines.
I've pondered for a long time an idea, that much of our human activity today is spent tending the growth of the machines and constructing our world to the benefit of the machines rather than the benefit of humanity. That's really what this series is about, machines telling humans what to do and the machines making humanity destroy itself to make room for the machines.