It is more "old school" than the Sigma 6 stuff, but bear in mind that the AE roster is decidedly smaller than it was back in the day. Most of the other characters are on "reserve" status, and don't have any part in that book. However, there is the Special Missions book that's published quarterly. A new one comes out in the next week or so, and the one before that had Beach Head and Cover Girl taking down a Cobra cel in Manhattan. The next one features Jinx in Japan, IIRC.
I'd start from the beginning, just to see how bad the Joes have it now, and to be hip to what Duke has been doing since he's listed as AWOL by Joe Colton.
Also, check out GI Joe Declassified. It's written by Larry Hama, and it details how Hawk brought the original team of 13 Joes together. It's bi-monthly, double-sized, and carries a pretty hefty price tag, but there will only be three issues and two of them have been published.
There's also Scarlett Declassified, a one-shot that came out last week, as well as Snake Eyes Declassified, but I haven't read that series yet.