You do know that it's possible to get touch of malice without that fragment right? Its just a temporary problem where you can't get this one particular fragment.
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I have 46 but the quest won't pop up so u do need this fragment
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Did you complete all the other steps before it? - need all the pieces from the raid quest - 50 hadium flakes, wormspore, and weapon parts farmed - 30 fragment quest done (undying mind boss) Also make sure the fragments were all found on one character. You can get all of them across different characters but you need the 45 fragments on one character to initiate the quest.
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Ya I have done it all
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I went through twice with someone and rechecked all available fragments. I should have 45 even without the charged rune. The only other one I don't have is one tier 3 from the court.Since I am unable to play destiny like its a full time job I missed one tier 3 several weeks ago. All I ever deal with is bungie nonesense.
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Agonarch rune is fixed now so this isn't particularly relevant anymore. Not sure if anyone else here has noticed but you can actually see exactly how many calcified fragments each character has found. If you select the dreadnaught orbit it will say "X/50 calcified fragments" just like the golden chests counter for the other planets. Hope this helps people track down the needed fragments to get their touch of malice.