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Starship: Flagship begins a few weeks after the events in Starship: Rebel. The Theodore Roosevelt, under the command of Wilson Cole, is preparing to lead Cole's ragtag armada into the Republic, even though he is outnumbered thousands to one. He is convinced that the government has become an arrogant and unfeeling political entity and must be overthrown.
The trick is to avoid armed conflict with the vast array of ships, numbering in the millions, in the Republic's Navy. For a time Cole's forces strike from cover and race off to safety, but he soon sees that is no way to conquer the mightiest political and military machine in the history of the galaxy. He realizes that he must reach Deluros VIII, the headquarters world of the Republic (and of the race of Man), in order to have any effect on the government at all - but Deluros VIII is the best-protected world in the Republic.
How can he approach it? Finally he hits upon the solution. Lafferty, his Republic contact from the previous book, controls a few hijacked Navy ships. The Teddy R "surrenders" to them, and they tow and escort it all the way to the heart of the Republic, to Deluros VIII itself - at which point all but a handful of volunteer "captives" move to Lafferty's ships, and then covertly land on the planet itself.
Cole's hand-picked crew infiltrates the governmental headquarters and ultimately confronts the Secretary of the Republic and Fleet Admiral Susan Garcia. Cole holds them at gunpoint and make his demands - and as he does so, a major power, not the Teroni Federation with whom the Republic has been battling for a quarter of a century, but a third power launches a surprise attack. AdmiralGarcia is killed and Deluros VIII looks doomed. Finally the Secretary makes an offer: if Cole will lead a successful counter-attack, the Republic will accede to his demands.
So the Teddy R becomes the flagship of the Republic's fleet, and eventually the enemy is defeated and the battle won. When Cole makes the Secretary's concessions public, it is clear that the Republic's days are numbered, that it is coming to an end (and as the timeline in each book shows, it is soon to be replaced by the Democracy). Cole is offered the Secretaryship, but he has spent his entire adult life bucking authority and has no desire to become an authority. Instead he recommends Jacovic, the Teroni who has personified competence and integrity, and indeed Jacovic is given the job, effectively putting an end to the Republic-Teroni Federation war.
With Jacovic installed and the Republic in its final days, Cole, the Valkyrie, David Copperfield, Sharon Blacksmith, and the rest of the crew depart in the Teddy R, no longer fugitives, no longer allied with the Navy, off to seek their destinies in unexplored sections of the galaxy (which leaves it open for a continuation of the series should that be desired.)