I went to the shop at the end of my street and as i got to the end i heared an odd sounding plane. I look up to see one with a red flare coming from one of the engines. It was going the opposite direction to the airport.
I wouldn't say they sort themselves out, but it is unlikely that your help is required. Air traffic control was probably aware of the situation before you were (and if they weren't, they definitely will be now).
Look around for a guy with a missile launcher, that may explain the flares. Beat him down, subdue him and reap in the money, fame, and the inevitable karma.
Yes, generally if I am out and about, and see something potentially sketchy, I rush to Bethesda Game Forums General Discussion section and post a query, about what I should do.