MIKE MOSS SAYS: Steve, I missed that story when it first came out. In looking over some news reports about the incident, no specific explanations were proposed regarding types of weather phenomena that may have led witnesses to report an unidentified object. The information available in news stories and columns, along with a quick look at weather observations from KORD and nearby vertical radiosonde balloon soundings, didn't lead me to any obvious conclusions. Weather conditions have been known to contribute to UFO reports, for example mirages (inverted, elevated or distorted images resulting from sharp vertical density gradients associated with strong temperature lapses or inversions), lenticular clouds (eerily smooth, often rounded cloud forms usually associated with shallow layers of moist, stable air flowing over rough terrain or sometimes over top of a thunderstorm). This story also mentions the craft accelerating away and leaving a clear hole in the clouds. There is a phenomenon called "hole-punch" clouds in which the passage of an aircraft through a layer of supercooled cloud droplets can initiate a sudden, circular clearing. In looking briefly at data from O'Hare and surrounding areas for the date in question, there was a low overcast reported at 1900 feet AGL. This layer would have been well above freezing and would not have been subject to the "hole punch" cloud phenomenon. It isn't obvious from nearby soundings that strong mirage phenomena would have been present, either, and lenticular clouds are typically at higher altitudes than would have been visible, and not favored in the flat terrain around the Chicago area. Bottom line, there wasn't an obvious weather explanation for the reports, but there isn't anything in the weather info that rules out some sort of weather explanation either.
Just for illustration, here are some addresses with lenticular cloud photos, some mirage imagery and explanations, and a couple of "hole-punch" cloud shots:
Also, for those unfamiliar with the UFO story, here's a column from the Chicago Tribune: