Alrighty, here we go. First things first, we're going to generate a list of mysteries, as of issue 5, all of which must be addressed by the final solution:

1: Who killed Sue Dibny?

2: Who told Dr. Light the JLA was after him?

3: Why is Batman in Dr. Light's flashback in issue 3, but not in the collective League flashback in issue 4?

4: Why is Calculator helping Boomerang reunite with his son/What "favor" does Boomerang owe Calculator?

5: Who attacked Jean Loring?

6: As Batman so aptly puts it, Who benefits?

7: Who is Boomerang Jr.'s real mother?

8: Who set up Jack Drake/Boomerang

The answers to 1,2,5 and 8 are clearly related, but not necessarily the same. The person who tipped off Light and set up Drake is the mastermind, but might not be the peron who physically killed Sue Dibny.

As to Question 7, there's also some debate about Boomer Jr.'s father, but there's a panel in issue 5 which, from the way their faces and particularly noses are drawn, makes it abundantly clear that Digger is the real father.

So what do we have? Someone who knew what the League had done, and thus that they would go after Dr. Light when Sue was murdered. Someone who is, or has access to, a teleporter or similarly powered assassin. Someone with something to gain from exploiting the Justice League's morally dubious actions.

It seems like the Suicide Squad is involved. Captain Boomerang, Dr. Light, Bolt and Slipknot all served, but then what C-list villain wasn't in the suicide squad at one point or another? So that doesn't really help that much. I'm also going to go ahead and not discuss the possibility of it all being a Sue orchestrated birthday mystery, or a mind-contorlling super-villain (where's the Ultra-Humanite when you need him?) because those are maddeningly stupid enough that I don't think DC would allow it.

The obvious answer, I think, is Calculator.

Calculator-
Pro: He's got his finger in enough pies to have orchestrated the whole thing, and the person outside Jack Drake's apartment is on a cell phone using the conversational tone Merlyn and Calculator have been sharing throughout the series. He probably stands to gain business from the whole ordeal, especially if he can eventually start selling off secret identities.
Con: Now that Boomerang is dead the story seems to be pointing at Calculator, which implies that it won't actually be him. Additionally, his involvement does nothing to explain why Batman has been erased from the memories of the JLA, or how he found out about this in the first place.

Chronos:
Pro: The guy can see the future/travel through time, which would make just about anything possible. According to the DC encyclopedia his arch-nemesis is the Atom. He keeps saying "we'll win" (which is creepy from an evil seer, by the way).
Con: He's barely in the series and doesn't seem to have much to gain.

Jericho:
Pro: He's a body jumper, and in issue 3 Slade delivers the Jericho jump-line "contact." Given the theme of family in the book, Slade's son is fair game.
Con: He hasn't even been mentioned by name, and Meltzer has promised he'd play by the rules.

Jean Loring
ugh, I hate doing this, because I don't think it's a hero and so far the only happy thing to come out of IC has been the reconciliation between Jean and Ray, but here we go:
Pro: Considered "safe" by the JLA security systems. Jean's story, as retold by Green Arrow in issue 4, doesn't jive with what we see in issue 3. There's a broken mug of coffee, in addition to the phonecall to Ray, which simply don't macth up with having just walked in the door and been attacked. Most damning is a panel on the second to last page of issue 3 which shows her gag being tied by hands from the front, not from behind. Could Jean have staged the attack?
Con: Why? Why why why? There's really just no motive.

ARGH! I've spent too long on this already and I don't feel like I'm cracking anything at the moment. My promise of an official declaration will have to hold off a little bit. The Batman thing is really screwing with me. Were the JLA's minds wiped as well?

Clearly Calculator is involved, the question is at what level. I feel so close, and yet so far.