So my friend and I have been keeping up with the whisper of the worm quests and just finished the last one, when we went to reshape it to upgrade it he told me he hadn't even started the witch queen campaign so he never had patterns or crafting unlocked. Because of this he never extracted the pattern for whisper so even after completing all 4 weekly exotic quests and unlocking crafting just now, he doesn't have any of the intrinsic upgrades, I've never dealt with this before so how would he go about getting them now.
Tldr; friend never extracted whisper pattern, completed all quests, doesn't have intrinsic upgrades now, how fix.
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I’d try using an alt character but unlock crafting first n it should than unlock on that character after repeating the process