The popular mechanics article is crazy and the incident is from 2004. They spotted an Unidentified Submersible Object larger than a submarine (a Virginia class sub is 377 ft long) with a UFO 50 ft. above it. The video of the FA-18's has the pilot saying "There's a whole fleet of them. Look at the S.A." The S.A. is the synthetic aperture radar which is a long range radar. In total, the UFO was picked up on radar by 4 F/A-18 and a Destroyer. The destroyer had been tracking the mysterious aircrafts for 2 weeks; they would suddenly appear at 80k feet then drop down to 20k feet then disappear off radar.
Personally, I think it's a government program. Perhaps a "swarm" type technology released by a submersible. Or Aliens *cue Ancient Aliens meme*
Could easily be advanced counter-measures equipment, especially if carried by a very light, small, autonomous vehicle during any possible visual engagement (it could not follow). I know the first thing I'd do if I was the DoD is trying to get some of our front-line military to engage it and see how they reacted.