Second Foundation is the story of the telepathic warlord known as The Mule and of the society of scientists, archivists, and clerks known as the Foundation. The book deals with the impact of exceptional individuals on huge groups of people, typified by The Mule's ability to alter the emotions of those in his surroundings. The novel also shows the curation of history by groups of the powerful, calculating, and oppressive.
Part I: Search By the Mule is about The Mule's search for the elusive Second Foundation, with the intent of destroying it. The executive council of the Second Foundation is aware of The Mule's intent and, in the words of the First Speaker, allows him to find it—"in a sense". The Mule sends two of his men on a search for the Second Foundation: Han Pritcher, who had once been a captain and a member of the underground opposition prior to being Converted to the Mule's service, and Bail Channis, an "Unconverted" man who has quickly risen through the ranks and impressed The Mule.
Channis reveals his suspicions about the Second Foundation being located on the planet Tazenda, and takes the ship there. They first land on Rossem, a barren planet controlled by Tazenda, and meet with its governor, who appears ordinary. Once they return to the ship, Pritcher confronts Channis and believes him to have been too successful with the search. The Mule, who had placed a hyper-relay on their ship in order to trace them through hyper-space, appears, and reveals that Channis is a Second Foundationer. Pritcher's emotional bonds to the Mule are broken in the ensuing exchange between Channis and the Mule, and is euthanized. With only the two of them left, the Mule reveals that he has brought his ships to Tazenda and has already destroyed the planet, and yet senses that Channis's dismay is only pretense. He forces Channis to reveal that Rossem is actually the Second Foundation, and that Tazenda is only a figurehead.
The First Speaker for the Second Foundation appears, and reveals to the Mule that his rule is over; neither Tazenda nor Rossem is the Second Foundation, and Channis's knowledge had been falsely implanted to mislead the Mule. Second Foundation agents are headed to Kalgan and the Foundation worlds to undo the Conversions of the Mule, and his fleet is too far to prevent it. In a moment of despair, the First Speaker is able to seize and change the Mule's mind; he will return to Kalgan and live out the rest of his short life as a benevolent despot.
Search by the Mule was originally published in the January 1948 issue of Astounding Science Fiction under the title "Now You See It—".
Part II: Search By the Foundation takes place 60 years after the first part, 55 years after the Mule's death by natural causes. Those of the (First) Foundation, which left the Mule's empire based on Kalgan after his death, are now aware of the Second Foundation's existence; although they, like the Mule, only know that it is located "at the other end of the galaxy", they know that it contributed to his defeat. Foundationists and many others believe that the Second Foundation's protection guarantees the success of the Seldon Plan despite crises, such as the Foundation's ongoing conflict with Kalgan. The ensuing war is won by the Foundation, and is listed in the Encyclopedia Galactica as the last major conflict before the rise of the Second Empire. Some Foundationists, however, distrust the Second Foundation and its members' Mule-like mental powers, and hope to find and destroy it.
After inventing a device that can jam telepathic abilities and cause telepaths great pain, the Foundation finds and kills about 50 telepaths on Terminus. The planet, the capital of the Foundation, is on the edge of the Milky Way. Since, as Arkady Darell puts it, "a circle has no end", then by tracing the disc of the galaxy around its edge, one would come back to Terminus. The Foundationists believe the Second Foundation destroyed, and believe that the Seldon Plan will proceed without interference by telepaths.
The telepaths however were nothing but martyrs taking part in a plot set by the Second Foundation to mislead the people of Terminus into thinking that the threat of the Second Foundation no longer exists, thus having the original Seldon Plan restored while its location remains secret. The Second Foundation is actually located on Trantor—the former capital of the Galactic Empire—in the center of the galaxy. It was called "Star's End" due to the ancient saying that "All roads lead to Trantor, and that is where all stars end". The location was also said to fit the "other end of the galaxy" location since the galaxy is not in facta disc, but a spiral—and from the edge, the other end of a spiral lies at the center. The book also noted that Hari Seldon was a social scientist, not a physical one. When the two Foundations were founded, they could be described as being at opposite social ends of the Galaxy, with Trantor at the very center of galactic power and prestige, and Terminus at the other extreme, something the First Foundation failed to realize because its members were inclined to analyze Seldon's statement in physical terms.
Search by the Foundation was originally published in the November and December 1949 and January 1950 issues of Astounding Science Fiction under the title "—And Now You Don't".
The Second Foundation would again be revisited in Foundation's Edge .