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After doing some digging on the matter, I think I found out just what the autistic boy did to get his gamerscore reset. It turns out there were some shenanigans surrounding the boy's acquisition of Recon armor in Halo 3.
This Spartan is lining up a headshot... on your gamerscore.
After piecing together some tidbits of information from the Twitter feeds of Xbox Live Policy Director Stephen Toulouse and the boy's mother, Jennifer Zdenek, I've figured out enough of what happened that I can probably fill in the whole story. [EDIT: Zdenek has removed her Twitter account since this blog was first published. I left the link in anyway, because I felt like it.]
Recon armor is pretty much the best thing you can have in Halo 3. It is a symbol of your domination of the game. There are two ways to get it: Bungie can give it to you directly because they think that you are awesome, or you can unlock a specific set of 7 achievements spread across Halo 3 and Halo 3: ODST called "Vidmaster Challenges." Some of them are pretty easy, like "7 on 7," the one for having 7XP in a multiplayer playlist on the 7th of the month.
Bungie really likes the number 7.I don't know why.
Others are quite difficult, like "Annual," which requires 4 players to beat the final level in co-op, on the hardest difficulty, with respawns turned off, AND without using a Warthog.
According to Zdenek, her son gave his account information to another gamer online (big no-no right there) who offered to get him Recon armor. Rather than earn them legitimately, though, the other gamer unlocked the Vidmaster achievements through external means* and returned the gamertag to the autistic child.
Since some achievements can only be unlocked online (such as most of the Vidmaster achievements), it's really easy for another player to see if these achievements are unlocked illegitimately, as they'll lack a timestamp next to them if they were unlocked offline.
This was likely brought to Microsoft's attention by an opponent on Halo 3 who saw the boy's armor. Maybe the boy underperformed in a game and someone thought he couldn't have the skills to unlock the armor legitimately. Maybe the boy cleaned up and a vindictive loser went looking for any dirt he could find to get revenge. Maybe someone is just skeptical of every Recon armor he sees. Who knows. In any case, someone likely compared achievements with the boy and discovered his Vidmaster achievements had been obtained offline, and followed suit with a complaint to Microsoft. Microsoft, upon receiving the complaint, saw the same thing and reset the boy's gamerscore, as is standard fare for people who cheat on their achievements.
STRANGER DANGER!! STRANGER DANGER!!
*I don't know exactly how one would go about cheating on their achievements, but I'm sure you can find out somewhere on the Internet. I could probably find it and link it here but I'd rather not give anyone any ideas or encourage that kind of behavior.