Gi Joe Origins was not intended to be a regular series, being a limited deal in its original incarnation. The five issue limited series was meant to be the 'genesis' of the Gi Joe team, as imagined by the brains behind its recent revival, and that was supposed to be that.
So when the Gi Joe relaunch began to sell like hotcakes, IDW decided to extend Origins into a regular series.
So this left us with a few 'out of sequence' issues, where we see the beginning of a few things going on in the regular book, such as Mainframe going rogue and a completely random mission with Scarlett, Stalker and Leatherneck.
And now, back to the plot.
These three issues pick up where the first five left off. Shortly after defeating Chimera, Hawk has decided the abandoned complex Chimera had holed up in would be a perfect place for his own base of operations, and has Breaker and Rock 'n Roll trying to rig up a minimal computer network to support the rest of the team, currently in the field. They're in Spain right now, trying to round up some Borovian extremists.
Borovia is, for those of you who haven't followed Gi Joe forever, a sort of 'placeholder' country in eastern Europe, a pretend land Larry Hama often uses to show Really Bad Things happening over there. Here, we see the brand new Joes are tracking down a group partially responsible for some sort of genocide that went down in Borovia - and once the Joes catch their targets, they realize they'd stumbled into something much larger.
This three-issue story arc has zero mention of Cobra in it, and that's perfectly okay - the Gi Joe team was built as an anti-terrorist organization first and foremost, after all, and it's nice to see them going after nuclear terrorists who aren't walking around in funny costumes for a change.
In fact, nothing 'fantastic' happens at all in this tale, giving the book a good grounding in 'reality'. Which sort of adds a bit of weigh to the weirdos in funny costumes you know they're destined to fight eventually... but it works.
You can likely track down all three of these issues at your local comic book store (for $3.99 a pop), or simply wait for the trade (which will likely include the aforementioned two 'filler' issues as well - IDW hasn't yet produced a comic it didn't yearn to cram into a trade paperback for you). Either way, it's a highly entertaining story featuring the 'core' of the 'new' Gi Joe organization.