Okay. So four kids get a security briefing, learn Morse code, travel to an island to take down an evil genius, and return to the mainland successful (more or less) but definitely affected by their adventures. Affected how? Well they've learned a few things "they all rather missed not knowing" (20.1), which makes us wonder if they'll ever be the same again after their mission. And the answer is no, they probably won't be. But they'll be okay.
We know this for certain because of the way the book ends: with the kids, all of whom now have solid families and friends, going outside for a snowball fight, and with Mr. Benedict reminding us (and himself and Number Two) that it's still appropriate for them to take time to play. Sure they just foiled a plot to take over the world, and yeah there's probably more for them to do (sequel set up), but "They are children, after all" (39.87). And that is a lovely note to end on.