Humanity rose from the ashes of the wars of the 23rd century as a changed species. Far more fearful, far more ready to put their fates in the hands of the new Emperor, a mythical figure who had finally ended the ravages of the century long war.
As time went on humanity discovered the hyperlane network, and expanded their borders rapidly. There were other space faring races, but the Empire soon brought them under control, forcing entire species to serve them as slaves.
Soon the whole of the milky way had been conquered, and the Empire turned inward to continue it’s never ending lust for power and control. The Shroud was discovered, and the aliens that lived there were analysed as best as the limited psychics under the empire's control could manage.
A nexus point was found, where a certain type of these shroud creatures seemed to “gather” at semi regular intervals. Studies showed that if these creatures could be contained, the Empire would be given access to so much power that they would be able to survive the heat death of the universe, by simply igniting their own stars.
A plan was formed, a trap laid. A device, half in the material, half in the shroud, was detonated the next time the creatures gathered at their nexus. Designed to imprison, the device was successful, and the species were contained.
The cost, however, was galactic in scale. From the half of the nexus device in our universe, a shockwave passed through both dimensions, ripping the hyper lanes from their anchor points and removing the ability to travel at faster than light speeds from the galaxy.
Now, 2200 years later, those hyperlanes have finally re anchored, in a new shape. Stars new and old are finally reconnected and those that survived the intervening years now venture forth to see what else is out there.
And the creatures from the shroud are waiting.
References
Stellaris: Nemesis Cold War VODs, Wiki Link, and Empire info (including prescripted empires file!)