The Section 31 Crisis was an attempted takeover of the Federation by the shadowy intelligence agency known as Section 31. It began in mid-2394 with the apparent deaths of Federation President Aennik Okeg and most of his senior cabinet in an attack by Tzenkethi rebels during peace talks to end the. He was replaced by his security advisor, and the only surviving member of his cabinet, Zothan Yix.
Admiral A. C. Zuriyev, then Director of Alpha Quadrant Operations, suddenly retired in November of 2394. He was replaced in that role by Admiral Smith.
In early 2395, both Vice Admiral Blackthorne and Captain T’Kirr were declared deceased following their apparent deaths in the destruction of shuttlecraft Naiad during a routine landing approach. The explosion in which they had apparently perished had been expertly staged to cover their abduction, interrogation, and imprisonment by Section 31 in its bid to gain control of Starfleet. For several weeks after their abduction, Blackthorne and T’Kirr were telepathically interrogated, with every single bit of information relevant to Starfleet forcibly extracted from their minds. Their subsequent release into exile was Section 31’s idea of a reward for their years of service, in lieu of execution.
With a command vacuum created by their ostensible deaths, Starfleet Command promoted Commander Kathryn Harper, Atlantis’s longtime CAG, to captain and commanding officer.
Captain Harper’s command ability would be tested only months later when she was faced with a flotilla of asylum-seeking Romulan Republic refugees attempting to cross the neutral zone into Federation space, technically violating the treaty in their flight from atrocities committed by the Romulan Empire. Her orders were to stop them by any means necessary, and she did just that; she negotiated a historic treaty with the fledgeling Republic, opening trade in exchange for providing food, medical aid, and assistance in rebuilding infrastructure. While publicly lauded for her diplomatic feat, Captain Harper was privately reprimanded by her superiors for brokering a peaceful resolution; the unspoken subtext that she should have stopped the refugees with violence was shockingly counter to the stated values of Starfleet, a fact that she found suspicious and deeply troubling. Harper, Atlantis, and her crew were placed under orders to be confined to Starbase Vinland until further notice, awaiting a punitive decision from Starfleet Command.
While sequestered at Vinland, Captain Harper was contacted by an informant with credible information that, contrary to official records, Vice Admiral Blackthorne and Captain T’Kirr were alive and being held as prisoners in exile on a primitive world. The shuttlecraft explosion in which they had apparently perished had been expertly staged to cover their abduction, interrogation, and imprisonment by a covert organization known as Section 31 in its bid to gain control of Starfleet. These revelations increased Harper’s suspicion of her recent questionable orders and, with the willing assistance of her crew, she chose to defy those orders in commanding the escape of Atlantis from Starbase Vinland.
As fugitives, Captain Harper and her crew proceeded to follow the trail of their abducted commanding officers, even raiding the Section 31 facility where they had been held in an ultimately successful effort to determine their location. After their rescue, Captain Harper returned command of Atlantis to Vice Admiral Blackthorne, having set in motion the end of Section 31’s attempted hostile takeover of the Federation..
In mid-2396, the Section 31 Crisis was resolved with the exposure and immediate dissolution of that organization after a coalition led by Blackthorne forced the President to allow the Federation Council to consider the evidence that they had gathered against Section 31. Blackthorne and the rest of the Atlantis crew were granted presidential immunity from prosecution for the justified but unlawful actions necessary to facilitate that outcome, and were also commended as heroes by the Federation Council, as were their allies. Vice Admiral Blackthorne accepted a promotion to full Admiral and Director of Starfleet Operations, and Captain T’Kirr accepted a promotion to Commodore and Assistant Director of Starfleet Operations.