Perhaps the most important theme in Spy Line is that a secret service agent can become involved in an operation that the agency may pragmatically decide depends on his death or imprisonment. In Samson's case the Department's open doubting of his integrity and loyalty is not merely a gross assumption based on the stupid notion of guilt by association, but the Department knows all the time that there is no reason at all to doubt Samson. The doubt is a mere ploy and nothing but misinformation to lull the Soviets into considering Fiona a legitimate defector. Although Samson's life is preserved, Fiona's sister Tess is cold-bloodedly murdered and fixed to be taken as Fiona to preserve the secrecy of the operation.

Another theme is that secret intelligence is inevitably linked to politics. A nation's foreign policy decisions depend on adequate knowledge, some of which may have to be supplied by secret intelligence, because politicians have to decide courses of action in regard to the capabilities and intentions of foreign nations whether they are adversaries or allies. Without politics, intelligence collection by governments would not be necessary.

A third theme is that it is more or less natural that experienced field intelligence agents become somewhat paranoid, but they do not become paranoid to the extent that they feel that no one can be trusted. Samson explains: "I am not paranoid. That is to say, I am not paranoid to the extent of distrusting everyone around me. Only some of them."

Lastly, there is the theme that the privileged class, or those whose origins are aristocratic and who are mainly Oxbridgians, are no longer morally or intellectually capable of governing Great Britain. Moral responsibility, know how, and talent must take precedence over inheritance. Samson's superiors tacitly acknowledge his meritocracy, despite knowing that his origins are middle-class and that he is a non-college man, when they consistently rely on his services because they feel confident that he can get the job done.