I asked Mr. DOA what significance bad code has in his world and he gave me a couple of explanations that went right over my head and didn't seem to fit the episode.
So we shall posit that Bad Code is modern lingo for Bad Seed.
In tonight's episode Finch is still in the possession of Root, the aforementioned Bad Seed.
We get some flashbacks of a night in small town Texas where a girl gets in a car and disappears. Reese and Carter are certain this is Root and go to investigate the old crime. Not only do they uncover what happened in the past, they show the good old boys who is boss and find out where Root currently is.
This showed some real mental agility that Reese hadn't previously revealed. I think he has been smart as a killing machine but has not been able to turn his mental skills towards good. Carter is a fine foil and is able to fill in some of the human elements and procedural methods that Reese doesn't have.
Any frame that Root is in is of course painful, whether she is using torture tricks on a government agent or just getting in Finch's face and being cooly slimy. I am really unhappy they let her get away, I do not want to see her again.
On the plus side, Reese figured out just where Root was holding Finch, got there just after they had left but he followed the breadcrumb trail Finch left for him of a cufflink and code typed into a cell phone...decoded the code at good speed, raced to the train station...rescued Finch, but let Root go when he could have easily gotten her. Grr.
Finch will now have that Dutch speaking watchdog as a companion. He accepts it even though the dog ate an Asimov rare title.
Kudos to the show for not quite going with the stereotypical librarian who was more than key to the disappearance of Not Root. The librarian was warm, friendly to everyone, but flawed in her choice of loves. Happens.