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In 2373, Admiral Whatley contacted Captain Benjamin Sisko to tell him that Bajor's petition to join the Federation had been approved. When he arrived on Deep Space 9, Whatley was irked by the fact that Sisko was on Bajor in the city of B'hala.
Whatley was one of the Starfleet representatives at the signing ceremony for Bajor's admittance into the Federation. Sisko's revelation of the 'locusts' destroying Bajor convinced the Bajoran Council of Ministers to delay their planet's acceptance of Federation membership.
Whatley later tried to convince Sisko to tell the Chamber he was mistaken but Sisko refused. Although Whatley threatened to have Sisko court martialled or transferred from Deep Space 9, he decided to abide by his decision, rather than facing the total loss of Bajor as a result of Sisko's removal from the station. (DS9: "Rapture")