To date, the total calcified fragments found are 47 out of 50. So obviously, 3 more fragments have not been found. Now, there are certain rumors that those three final calcified fragments will be discovered when hard mode of King's Fall Raid comes but, it looks like all those rumors are just rumors after all. Not even a single fragment were found in HM so this leaves many Guardians questioning... Where are the final three calcified fragments?
A few days ago, Luke Smith confirmed that a Challenge mode will be added to King's Fall Raid, in an offhand comment first spotted by More Console. According to Smith, each of the three main boss fights in King’s Fall – Warpriest, Golgoroth, and Oryx – all have an added challenge – a special way of killing them if you will – that will unlock unique rewards and a new emblem.
The addition of a new challenge on King's Fall is a good news but, the better news is the unique rewards and new emblem. Even better, thanks to Smith, we now know that the last three calcified fragments are locked behind these Challenges which are not yet active. Although Luke Smith promises more info about these Challenges will be shared "in several weeks," he did reveal that at least part of these rewards will be the final three Calcified Fragments.
Finding these Calcified Fragments is actually part of a questline that ultimately rewards you with the highly coveted Touch of Malice (which requires you discover 45 of them). We don't yet know what discovering all 50 will reward you with, but I'm fairly positive it'll be another powerful Exotic item.
Challenges being time-gated is just another example of Bungie's goal in year two to not only keep Guardians invested in the game, but to also limit the randomness of acquiring certain Exotics. Like Sleeper Simulant and Black Spindle, completing these Challenges will probably be a mystery. However, once you discover how to complete them, you'll probably be rewarded quite nicely.
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