Craft shows up out of nowhere and tries to destroy Federation HQ (he's at war with the V'Draysh remember), but is only stopped by the appearance of Discovery, which he recognizes. However Discovery and the sphere data have no idea who Craft is (wibbly wobbly timey wimey), leading the crew and Vance to realize, to their horror, that to preserve their timeline they have to break the ban on time travel, as they now know Discovery has to be sent back in time 1,000 years to explain Craft's recognition.
Vance reluctantly allows Discovery to be sent back in time. However, an assimilated Detmer (who looks like a Borg anyway) was aboard when it was sent back, and Detmer thus becomes the first Borg queen (meaning the Borg have no origin and in fact are a temporal ontological paradox).