Hopefully you've read BATMAN #10 by now. Since the "New 52" started, we've seen Bruce Wayne dealing with a long hidden mystery in Gotham City. He thought he knew everything about the city but soon discovered the existence of the Court of Owls.
The Court stemmed from an old nursery rhyme. After Thomas and Martha Wayne were killed, Bruce wondered if there was more to their deaths than a simply mugging. Investigating the possibility of the existence of the Court of Owls lead him to the conclusion that they did not exist. This was an error that would soon come back to haunt him.
In the first nine issues of BATMAN, we've had mystery after mystery. Revelations have been sprouting left and right but none have been as huge as the one in issue #10. We now know the answer to the question of who has been behind a lot of the recent events.
This revelation changes the history of the Waynes as we thought we knew it. Scott Snyder made a bold move in firmly establishing this as an official part of Batman's mythos. This is why it makes perfect sense.
Final warning: there will be spoilers below!== TEASER ==
The idea that Bruce Wayne had a brother, Thomas Wayne Jr. isn't a new concept. Those opposed to the idea of Bruce having a brother can't accuse Snyder of changing history because it's an idea that was established. Only nothing was ever really done with it.
The main source for Thomas Jr.'s existence is WORLD'S FINEST #223 from 1974. Batman was on the hunt for the Boomerang Killer. Along with Superman and Deadman, Batman was determined to find the killer. Deadman, inhabiting a civilian's body, managed to follow the killer to an apartment. When Batman and Deadman entered, they found a notebook with the name, Thomas Willowwood.
Deadman pointed out that Willowwood was the "upstate funny farm." Willowwood was also the name of the facility in BATMAN #10. Obviously there would have to be a reason for a patient at Willowwood to have that name as their surname as well. When Batman (and Deadman) visit the sanitarium, the doctor informs Batman that he can't give him access to Thomas Willowwood's records but is able to tell him that he escaped about a year ago. As for why his last name was Willowwood, the doctor informs them that Thomas came to them as a child and the name was used because his family name is a secret.
With Deadman able to inhabit people's body's, he jumps into the doctor's after Batman says there's no time to get a court order. As much as Batman dislikes using these methods, the killer is still on the loose. He reads that Thomas arrived there as a small child and was insane from injuries resulting from severe trauma after a car accident.
It's unfortunate that Thomas is still disturbed. It turned out that he was being used to kill others. The real killer convinced Thomas that the victims were enemies that were out to get him. Thomas seemed to have disappeared but what happened was Deadman took over his body and left. With Deadman in "control" of Thomas' body, innocents couldn't be harmed and Deadman had a new body for himself.
What doesn't make sense is the very next story in the same issue makes no mention of Deadman taking over Thomas Jr.'s body. He's back to his normal routine of randomly taking over people in order to get to the bottom of things. What ever happened to this Thomas Jr.?
Of course this isn't the only Thomas Wayne Jr. we've seen. In the reverse world of Earth 3, Thomas Wayne Jr. exists as Owlman and is part of the Crime Syndicate of Amerika. It was made that Owlman was Thomas Wayne Jr. in JLA: EARTH-2, published in 2000.
The character, Owlman, in the Crime Syndicate is meant to be the opposite of Batman. You could say he's his dark reflection. But this isn't simply an evil Bruce Wayne.
Owlman is actually Thomas Wayne Jr. on his world. Instead of Thomas Sr. and Martha getting killed, it turns out that Martha and Bruce were murdered. Thomas Jr. blamed his father for their deaths and became Owlman while Thomas Sr. became the commissioner.
The key here is the fact that Thomas Wayne Jr was Owlman, totally fitting considering Lincoln possibly being Thomas Wayne Jr and his connection to the Court of Owls.
In other words, Snyder didn't simply re-write history and introduce a (possible) brother to Bruce Wayne just for shock value. The existence of Thomas Jr. already existed. For whatever reason, absolutely nothing was done with it. Bringing him back could have been done by anyone. Thankfully and obviously Snyder put deep thought into how to make it work and work so well.
We'll have to keep reading to see how these events play out. Bruce doesn't fully believe the confession but he was wrong about the Court's existence in the first place.