Making a secret plan or scheme, usually with others; or marking points on a graph to show data.
From Middle English 'plotten,' possibly from Old Norse. The sense developed from marking positions (on a map) to planning positions and sequences (as in a conspiracy).
The same word describes both what a spy does (plotting against the government) and what a scientist does (plotting data on a graph)—they both involve mapping out hidden relationships that become visible when arranged correctly. It's the same mental action with different consequences.
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