After altering reality so mutants were the dominant race, the Scarlet Witch then changed reality again, this time attempting to rid the world of the mutant gene, by casting another spell, "No More Mutants", de-powering the vast majority of mutants.
Initial count, oversimplifications & errors
In total, 986,618 mutants were either depowered or killed by the Decimation.
At the time of the Decimation, it was first estimated that 91.4% of the world's mutant population lost their powers overnight. The US Government estimated a number of 198 mutants, cataloged, but acknowledged that there were a few thousands, around 300 individuals who were recognized as mutants, and Tony Stark admitted that a low estimate had been produced. Dani Moonstar stated that there were 198 known mutants, but others had remained off the grid until then, including Jonas Graymalkin or Leon Nunez, but also known mutants, like the "199th mutant", off the record of the 198 as part of a deal with the government, or Wiz Kid who hacked into S.H.I.E.L.D.'s database.
The 198/"less than 200" estimation was although often used as the correct number, as well as "9/10" or "two hundred remaining mutants". A Cerebro estimated a decrease of 91.4% of the world's mutant population in the moments after the M-Day, when Tony Stark stated (after the Civil War) that over 99.99% of the mutants were. It was often stated that "90%" or "over" of the mutants lost their powers.
Many mutants thought to be depowered were later revealed to have maintained their powers, having hidden their mutant powers and/or their presence to the world, while many of the still-powered were killed during the violence that followed the Decimation.
These different counts, along with the low number of individuals using their powers in public made some calculations very risky and absurd:
- At Matt Landru's funeral (one of the 198), Bishop stated that 10 percent of the world's mutants were present.
- The twenty-five students of the Xavier Institute represented about one-eighth the mutant population in the world. The sum of the mutants of the Institute represented one-quarter of Earth's mutant population when Hulk attacked.
The 198 at the Institute
The Xavier Institute became a haven for those who still had their mutant powers, many of them attempting to escape persecution. Against the wishes of Institute professors Emma Frost and Scott Summers, the government assigned Sentinel Squad O*N*E to protect the mansion and its inhabitants.
Reporter Sally Floyd interviewed a number of depowered mutants for her Mutant Diaries report. However, a serial killer calling himself the Ghoul murdered several of those whom she interviewed, leaving "Not enough died" as a marker. The Ghoul was eventually killed in an explosion during an attempt to capture him by the X-Men. Given the nature of his teleportation powers, it's possible that the Ghoul survived.
M-Day Energy Effects
When Scarlet Witch depowered mutants, she did not destroy the energy those mutants possessed. Instead, the energies got expelled from their bodies. While passing some orbiting rocks, the energy awakened a dormant Vulcan (who was able to survive in space due to being fused with Darwin). This massively boosted Vulcan's powers. Eventually leaving orbit and entering the atmosphere, the energy was absorbed by the Collective, turning him into an immensely powerful and dangerous being; the energies later got dispersed into the Sun.
X-Cell, a group of former mutants who blamed the United States government for losing their powers, began a terrorist campaign. With the overwhelming majority of Mutant Town's residents now depowered, the label quickly began to lose all meaning.
Salem's Seven's return
Frightened by the end of mutantkind, Beast went on the search for a cure.
Effects on Multiverse and non-natives Mutants
Almost all mutants from alternate realities residing in the Earth-616 reality retained their powers (i.e. Bishop, Dark Beast, Rachel Grey, Sugar Man, etc.), but this was just a coincidence, since Jon Spectre lost his powers. There also appears to be some confusion about M-Day's effects on the Multiverse.
According to Forge there were no more mutants in the entire Multiverse. Using a combination of Cerebra's and Nimrod's technologies, he showed to Beast that Age of Apocalypse's, Nimrod's and Bishop (Earth-1191)'s timelines were shut down or empty of mutants. After the birth of Hope Summers, two future timelines with mutants suddenly became active again: Earth-1191 (which was earlier "shut down") and Earth-6124. Numerous X-Gene positive alternate realities have been seen since then, indicating that Hope's existence reversed M-Day on a multiversal scale, not just in Earth-616.
Reversing the Effect
While the M-Day effect was initially thought to be irreversible, some methods proved more or less effective in restoring mutant powers. Please consult the Repowered Mutants and the ways they got their powers back.
In concordance with the High Evolutionary, Magneto was able to construct a machine to restore his powers, using the Dreaming Celestial and the product of what they called "a Celestial lobotomy". The machine however, was not only nearly impossible to construct but extremely dangerous. The process worked, and Magneto regained his mutant powers at the cost of the machine itself.
Apocalypse managed to restore the powers of Polaris (depowered by M-Day) after turning her into a Horseman. It was believed that Apocalypse simply gave her powers similar to her old ones through other means, but he seemingly managed to re-activate Polaris' X-Gene.
After one of Legion's rogue personas, dubbing itself Moira, altered reality to create a world of constant war and struggle where he was a hero, some aspects of this reality bled through into the real world after Legion restored it. One of these aspects were the powers of Chamber. In this reality created by Legion, Chamber once again had his mutant powers in their old state, and upon returning reality to it's original form, Chamber kept his restored powers.
Hope Summers and Phoenix
The return of mutant messiah Hope Summers to the present triggered the first activated mutations since her own and M-Day. It is believed that this, along with Hope's unique ability to stabilize these mutants, were an extension of her relationship with the Phoenix Force.
The Phoenix Force travelled to Earth to claim Hope Summers as its host in order to reverse the Scarlet Witch's curse. It did so successfully, after Hope used its powers to re-ignite mutations across the world. This only caused new mutant births however, and did not restore the powers of previously depowered mutants.
After the founding of the mutant nation of Krakoa, a group of mutants known as the Five were created, composed of Hope Summers, Proteus,Tempus, Egg, and Elixir. The Five were tasked with resurrecting mutants who had died prematurely. The Five able to revive depowered mutants with their powers intact, presumably in part due to Proteus' reality warping powers. 
List of confirmed powered or depowered mutants post-M-Day
Among the unnamed powered mutants to be counted are Gargouille's boyfriend and a fire-breather, both killed by Predator X. Utopia and Ravencroft Asylum for the Criminally Insane also appeared to had various unidentified mutants.
Known Pre-M-Day Deceased Powered Mutants
The Decimation extended even to mutants who were already dead on M-Day. When Selene reawakened the dead of Genosha and elsewhere, she discovered that many of her undead subjects no longer possessed their mutant abilities as a result of M-Day. Please consult the Known Pre-M-Day Deceased Powered Mutants.
Please consult the M-Day Depowered mutants.
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