The Super-Sons head to a little town with a big secret in World’s Finest 216 (Feb/March 1973). In fact, that’s even the title of the story.
This story, by Haney, Dillin and Murphy Anderson, is the first in which the Super-Sons carry a tale without their parents. Superman and Batman appear only on the cover, and in the looming figures on the splash page. Of course, that may actually be them, hovering above. The lack of confidence they have in their sons means it wouldn’t surprise me.
The boys have been biking across the country for a while. Long enough to be getting on each others nerves, despite their friendship. Superman Jr can fly, but often prefers not to. Part of establishing the lower power level than his father.
So anyway, the boys wind up in this sparsely populated town, where the people who are left act all creepy and hostile. The boys get tossed into prison.
Superman Jr discovers a huge cryogenic storage area, with most of the townspeople in it.
We discover, along with the Super-Sons, that aliens had landed in the town. They wanted to live there for 20 years while their ship repaired itself, and would then offer them all manners of riches. The townsfolk lynched them, and then started putting themselves in cryogenic suspension to emerge when the ship opened.
There’s even a second criminal plan, with one man who has figured out the real date trying to get all the townsfolk frozen. The ship finishes its repairs and simply bolts. The townsfolk are left to deal with what they have done.