First, a list of the pending mysteries: Sivana's photonic crystal. The identity of the headmistress. The detail that Ra's says that Talia forgot. Whose death causes the second headstone in Bruce's vision? And overall, just where is this going?
Oroboros, Otto Netz's invention that allowed him to build a meta-bomb, a ring around the world, and Sivana's photonic crystal are both meta-materials. Unlike many comic book gadgets, these actually exist, and on small scales, actually do allow such otherwise impossible properties as a lens that pulls out detail smaller than the wavelength of the light that passes through them, and as mentioned in the comic, invisibility. If the importance of this is simply to give Batman one more weapon in his coming battle, then this will have its role, which should pass quickly. However, as this was introduced in the first issue of Inc, and has been mentioned more than once since then, it probably has a larger importance, related to the meta-bomb threat rather than as a mere battlefield weapon. The common language used to describe both and the explicit comparison of the two seems like more than coincidence.
The headmistress from Leviathan Strikes has been conspicuously hidden from full view in each appearance. We see her once with black nails, once with red. She wears a revealing dress in #10, and we find out that she's on Batman's side while she appeared to be on Leviathan's. And with the girls she trains wearing costumes in the style of the original Batwoman, others have guessed that she indeed is Kathy Kane, the original Batwoman whom Morrison has shown at several intervals in his epic. As of Inc v1 #3-5, she has been rewritten as a double spy, who was asked to betray Batman, and began that assignment but did not complete it. We know that Scorpiana is an underling of the headmistress, and we know that both Kathy Kane and Scorpiana dance the tango of death. Batman seems confused about the true identity of the headmistress, and he also seems convinced that Kathy Kane really is dead. Overall, the pattern is most easily completed if it turns out that Kathy Kane faked her death and has been seeming to work for Leviathan but will now fall in line and come to her former lover's assistance. For her to seem unscrupulous and turn out to be something more was even foreshadowed back in Batman #682, when Morrison's "Last Rites" story showed her leaving Bruce, prompting a young Dick Grayson to say, "There's something about her I don't trust." At the end of Leviathan Strikes, we see a woman speaking to Matron (the head of Spyder) about the death of Netz, and about her obvious familiarity and hatred of him, a hatred well explained in her recruitment into Spyder by Netz, who claimed to be her father. This woman has the Fifties hairstyle Kathy Kane was known for; it seems clear that Kathy Kane remains high up in Spyral.
Kathy Kane's death at the hands of the Sensei's men is a curious fact for Morrison to reference. The original Batwoman nearly disappeared from DC continuity in the early Sixties, but made a very brief appearance in which she was killed in 1979's Detective Comics #485. A fact of that story, which I will mention later, may prove to be a key plot element still to be seen in this one.
In Inc v2 #2, Talia visits Ra's, at his request. He announces that she will remain his prisoner, but she turns the tables and makes him her prisoner. The issue is full of flashbacks summarizing the history of Ra's, Talia, and Batman. The battle of wills between father and daughter is full of betrayals and reversals, recapitulating the events of #2 itself, in which he forbids her to fight a war against Batman, which seems only to strengthen her resolve. We don't see Ra's again until #10, in a scene that borrows atmosphere from the famous Batman-Joker scene in The Killing Joke, and again in DC Universe #0, when a captive foe seems to hold power over their captor. Just as the Joker plays cards by himself in both those scenes, Ra's plays chess by himself in this one.
The details of Ra's's chess game are obvious allegories to the main action, with red representing Talia's side (she wears red through most of #10), and black representing Batman's. First we see a red rook capture a black pawn. This is the Heretic killing Damian. Damian is even referred to as a pawn in #2. This is followed by a move in which the dark knight captures the red queen, and the meaning of the dark knight should require no explanation.
Multiple clues point to the fact that Ra's is not actually a prisoner at all, except in the literal sense. For Talia to have been revealed as the villain in this story came far too early, when the story has yet to climax.
1) In the aforementioned Detective #485, Ra's visits Batman and tells him that the Sensei was behind Kathy Kane's murder. He later says explicitly that he did so in order to use Batman against Sensei, so that the battle will weaken both of them, leaving him to emerge victorious.
2) The chess game itself, representing Batman and Talia is literally being played by Ra's. In that the pieces represent other people, we are seeing Ra's as the main agent, using others (as when he "forbids" Talia from fighting Batman) to weaken one another. In Detective #485, this was against Sensei (retroactively defines as Ra's's father by Morrison). Now the same dynamic skips a generation, with Ra's working against his daughter. Clearly he ends the scene smug, in control. His control is likely to become the central fact of the story's climax.
In addition, there is a very cagey geographical detail in the story which is unlikely to be a coincidence. The setting of Ra's's imprisonment is in Switzerland, by a mountain called Jungfrau, German for young woman. This mountain is invariably considered one of a trio, along with the Eiger (Ogre) and Mönch (Monk), all visible in one panoramic sweep. These map onto the key players in the story with Batman as the Monk and Talia as the Maiden. Perhaps the brutish and powerful of the Heretic indicate that he represents the Ogre, but the legend implies that the Ogre is a threat to the Maiden, whereas the story (and the chess symbolism) indicate that Heretic is a mere physical force serving Talia, alternately the Queen and the Maiden.
For the story to end, we also need another death to take place, one that makes Bruce mourn greatly, and for him to place a grave on the grounds of Wayne Manor. The best fit for this may be Kathy Kane, who could die as soon as she returns, just as she did in 1979.
Ultimately, something big is at stake. The battle with Talia is due to begin at 11 o'clock and what is 11 o'clock but an occurrence before the climax, which Morrison has twice (once with the Joker, once with Doctor Hurt) set at midnight. Morrison has also made mention of midnight in reference to Darkseid and Mandrakk. 11 o'clock is a pointed choice on his part to say that Bruce's battle with Talia is not the climax, but the thing that comes before the climax. We've seen enough mention of apocalypse and the Devil to wonder if the Heretic, Fatherless, is that climax, and yet Heretic appears simple, easily dominated in a battle of wills despite his enormous physical power. Ra's, on the other hand, looks calm and collected, and calling the shots. The endgame, the midnight battle, may show us what happens between Batman and Ra's once Talia has served her purpose as Ra's's tool.