Have you tried drawing a line from the 'something' to the helicopter(s) and checking the cities close-by?
Even cars/vans/hummers have a somewhat passable base detection radius (3-5 times the radar circle). The fighters and transport planes can have continent-spanning detection.
Off-topic, but IMO this is silly, and I removed detection from what's essentially someone else transporting you, and slashed base detection compared to on-board radar for actual aircraft. Because how exactly do you spot one house among millions? Radar at least has relatively fewer targets, clear hostile trajectories and transponders for civilian craft. Not to mention the air game is less interesting if everything has a biggish radar. That's what probably killed the AWACS.
Finally, if you're bored of checking cities one by one and the bases no longer really challenge you during that, what I do to skip the tedium is make a waypoint, copy the base coordinates over from 'alienBases' and use that to check the right spot.