Best You Can Hope For
AN: originally done as a response to the YJ-Anon-Meme. De-anoning like a boss.
Standard Disclaimer applies - I'm not DC, I don't own Young Justice or anyone therein.
Ever since the Cadmus incident and the discovery of project Kr (current codename: Superboy), Batman has known it's a distinct possibility that each and every member of the Justice League could have been compromised in a similar fashion. Robin's disturbing rundown of their decision to download their memories, clone and replace them practically on the spot during his debriefing only led further credence to what would, under other circumstances, sound like the stuff of completely paranoid delusion. It made him wonder for quite some time after that if it would even be possible to tell the replacements from the originals (and, in the most haunting of nightmares, if his Robin had ever returned from that facility at all).
There were, of course, things Batman could do to make things more secure against this type of internal threat. Updating his plans to take down each and every member of the Justice League with the new members and the profiles of the Young Justice team is merely the first phase. Tightening the Watchtower mainframe's security, as well as the Manor's own, with increased security algorithms is the second step and unfortunately, as he well knows, a long-term project. He has Robin join him in training their minds to lock away information they don't want known and how to do this under duress similar to what Robin had experienced in the Cadmus Facility (Dick has nightmares, sometimes, after this training, but Bruce stays close and, sometimes, if they are lucky, Batman does not search Dick's exposed skin for the scars Cadmus wouldn't have had time to replicate).
Batman spends whatever time he can afford to look for links to Cadmus. Facilities like that cost money to run – lots of money – and it had to come from somewhere. Luthor is an obvious choice, but perhaps too obvious. Ra's is another likely candidate. And then there are the unknown players, the wild cards. There are a lot of people who'd like the Justice League either in their pocket or quietly disposed of. Certainly, more than one military organization would sell their souls to get their hands on even a quarter of the technology available to the League, and it wasn't like they hadn't stopped some particularly unsavory attempts at duplicating the powers of metas in the past. A lot of their problems would be solved if the Justice League were suddenly and inexplicably programmed to be a little more amenable to sharing.
And as he is the most secretive, the most private with his technology, Superman's best friend, and the man with the keys to all the doors in the Watchtower, it only makes sense that Batman would be the logical choice to clone as well.
So, when the disc arrives on his desk, he is not surprised completely at the contents.