I would think Ouruboros would help with that, available by about level 35, it lets you use old Missions you might have missed/ out leveled.
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Currently there is no way to go back and play through the Praetorian mission content again, though the badge description seems to indicate that adding the Praetorian arcs to flashback/Ouroboros is in the cards somewhere down the line. For now, your best bet to earn the badge is to turn off xp and run another mission arc before outleveling.
You can't reestablish your ties with the Resistance or Loyalists later (for the forseeable future), but there are a couple of arcs in the 40-50 range that deal with the Praetorians, and much of the 50+ Incarnate content is focused squarely on pushing back the Praetorian invasion. Specifically the Apex and Tin Mage TFs and the new trials coming in I20.
There is an art, or, rather, a knack to flying. The knack lies in learning how to throw yourself at the ground and miss. --The Hitchhiker's Guide to the Galaxy
For the badge: You don't. There are 13 moral choice missions in Praetoria. At the moment, you have to get to 5 of them before leaving if you want it. However, if you look closely at the badge hint, it mentions Flashback in there. I suspect that they plan on adding Praetorian missions to Ouroboros at some point, or possibly a special Praetorian Ouroboros zone.
As to the return to Praetoria: No. Praetorians get different mission text in some of the new missions from native Primals, but at the moment, there is nothing special for Praetorians once they've left Praetoria. In the future, maybe, who knows...?
@Roderick
... and stuck with a badge that says "Complete five Praetorian Moral Choices to earn this badge." 4/5
How do I go back and wrap this up?
Also, I felt a bit let down that it just pushed me back into the regular City of Heroes storyline - do we ever go back and help the Resistance and fight Cole or whatever path we were working on?