Flame was discovered in 2012, linked to Stuxnet, and believed to be American in origin. It has recently been linked to more modern malware through new analysis tools that find linkages between different software.
Seems that Flame did not disappear after it was discovered, as was previously thought. (Its controllers used a kill switch to disable and erase it.) It was rewritten and reintroduced.
Note that the article claims that Flame was believed to be Israeli in origin. That's wrong; most people who have an opinion believe it is from the NSA.