Flying Spaghetti Monster wrote:
I always wondered at exactly what point Marcus and Khan stopped being allies. By extention, I wondered why Khan beamed to Kronos at all.. was he personally interested in having the Federation start a war with the Klingons?
This is how I'm remembering those events:
Admiral Marcus and Khan were never allies. Marcus was holding the other 72 Augments as hostages to ensure Khan's cooperation with him and Section 31. Khan found them, and tried to hide them by placing their cryotubes inside torpedo casings. But Marcus figured out what Khan was doing and he took the tubes. Khan went apeshit when he thought Marcus had killed his "family," and that's why, after his attack on Starfleet which resulted in Pike's death, yes, Khan went to Kronos to start something between the Klingons and the Federation. He changed his mind once he'd realized that the cryotubes were still inside the torpedo casings where he'd left them.
Even if Marcus had gotten Khan to agree to help him without resorting to extortion, I expect that Khan would have betrayed Marcus anyway, just as soon as the usefulness of their faux alliance had run out. Not unlike what he does with Kirk later on.