This is one of those entries that deserve an animated short. The struggle of the Qugu and Te'Qal and how everything ended made me oddly emotional for some reason. Not gonna spoil anything in the main body here, if you haven't read it, definitely give it a read. Minor spoiler warning below though.
[spoiler]The Witness was definitely threatened by the Qugu's evolution and darkness mastery to have 🐔 blocked their fight against the Hive. If the Pyramid didnt intervene and they discovered Resonance sooner, there would be no Oryx or Savathun. MF's killed a Pyramid with a tiny fleet of ships AND earned the Witnesses respect[/spoiler]
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[spoiler]It was more like, once the Pyramid was pierced through, the Witness triggered a wave of Resonance to wipe out the remaining Qugu, and simultaneously offer Te'Qal and the Qugu "Salvation" through being made part of the Witness' gestalt being as a memory/Echo.[/spoiler] It does greatly recontextualize why the Qugu, and perhaps certain other races, would have been included in the Books of Sorrow, where they were originally just names as one of the races among the Hive's conquests. The Ecumene also had a lore entry for them in "Inspiral" that revealed their connection to Darkness, just as the Qugu had their own. It wouldn't surprise me in the slightest if one of the future Echoes is connected to the Ecumene - the memory of the race that nearly brought an end to the Hive, if not for Oryx gaining the Taken power.