We know the Endless and/or the Xalanyn are ancient beings, older than Forerunner civilization. The only other beings we know that are that old are the Precursors, as they seeded life in the Milky Way and were the sole creators of the concept of the Mantle of Responsibility. Could it be that the Endless are extragalactic beings much like the Precursors? Did they come from an outside galaxy to lay claim to the Mantle, thus being perceived as a threat by the Forerunners? Just as the galaxy is being re-fed life after the Array Fired, this alien species comes in, already fully advanced, and plans to take the Mantle for this new Galaxy for themselves. They may have also been created by the Precursors. They could be an example of what the Forerunner empire could’ve been had the Flood not been created.
That would also explain why the Forerunners were not aware of them beforehand despite a 10 million year rule of the galaxy, because the Endless are not from the Milky Way.