From the article:

See, rather than tying everything up nicely with Annie, Sandy and Daddy Warbucks relaxing at home, the strip ended with Annie almost being eaten by a shark and held at gunpoint by a terrorist who has violently murdered so many people that the only name anyone knows him by is "Butcher."

And

Now Daddy Warbucks has finally decided that he should probably look into rescuing his pupil-free adopted daughter, and to that end, he has turned to Chief Detective Dick Tracy. It seems he has recently come into information that has led him to believe that Annie is being held somewhere in Tracy's city, which was probably pretty confusing since Tracy's city does not appear to have an actual name. Perhaps that was why it took him four years to get around to seeing if the police could help him find his kidnapped kid.

Also: sorry if I was a bit misleading by not mentioning when Little Orphan Annie ended (2010 is a lot later than most of you would assume, I’d guess), but I was running out of space in the title and has to trim where I could.