The story is based on the 1988 Batman Comics storyline "A Death in the Family," where readers voted via a 1-900 number to either save or kill off the second Robin, Jason Todd. Over 10,000 votes were cast and with only a 72-vote majority, the decision was made to kill him. Todd was later brought back in 2005 as part of the 2005 "Under the Hood" storyline.
In every flashback showing Batman, the costume has minor differences (like the yellow chest symbol and older utility belt style), which is consistent with the fact that Batman does update his equipment and costume as he regularly fights for justice.
Although Batgirl/Barbara Gordon is not in this film, she is referenced when Jason Todd mentions to Batman about "friends The Joker has crippled."
The film was originally going to be R-rated, but due to the low sales of the previous DC animated movies, Wonder Woman (2009) and Watchmen (2009), under performing at the box office with their own R-ratings at the time, many Warner Bros. studio heads ordered that Bruce Timm and his animation department complete several edits to make this movie PG-13 and more accessible to children. Some action scenes were shortened, most gory scenes were removed entirely (i.e. - the severed heads of the mafia leaders was originally going to be shown instead of only being implied), and a lot of excessive blood effects were scrubbed away (most notably during Robin's death and post-death scenes).
The opening sequence in which Batman is carrying Jason's dead body out of the rubble is taken directly from the comic book.