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I have been reading the new monthly G.I. Joe and G.I. Joe Special Missions and I am slightly puzzled. They seem to hint towards some sort of betrayal by Snake-Eyes to the G.I. Joe team. There is a brief flashback in a dream Scarlet is having where she seems to shoot and kill Snake-Eyes.

Did I miss something in another series?

I'm still trying to catch up on all of them, but I noticed that too. Haven't come across what happened - but I did skip a bunch of TPB's.

The latest series is a continuation from the original storylines started in 2009.

From wikipedia:

In 2009, IDW Publishing began to publish the series again. IDW's G.I. Joe series is a complete reboot of the property, ignoring the continuity from the Marvel and Devil's Due incarnations of the comic. However, the G.I. Joe: A Real American Hero series originally published by Marvel Comics in the 1980s and 1990s was revived as an ongoing series in May 2010 with a special #155 ½ issue, and followed by #156 onwards in July 2010. The series directly picks up from the end of the Marvel Comics series and ignores the Devil's Due continuity completely.

Here's the IDW specific wikipedia article:

http://en.wikipedia.org/wiki/G.I._Joe_%28IDW_Publishing%29

BTW: While I collect the G.I. Joe issues, I'm only reading the trades and am very behind on what's current. I just hope these references help you out.