You wake up. You are a jaguar with all the memories and skills of a ninja. Your old clothes are shredded and scattered around the den. There's a little bit of blood. Using a combination of your ninja tricks and jaguar advantages, you scale the pit in the dead of night. Time to complete your mission.
From here the plot might tak you anywhere, probably do some jungle training, some aztec temple cultist hunting, and ultimately sneaking back on the boat to Japan for the second half (?) of the game.
Gameplay: stealth action, ala Assasin's creed, with less stand-up fighting, but more intimidation. A lot of stalking prey, frightening gardeners, revealing yourself at just the right moment, and biting people in the neck. Probably ideal for Xbox 360, you have a growl button, a pounce trigger, a swat/bite trigger, and a climb/freerun button, and a stealth button. Or stealth is your default mode, more likely.
The final missions involve assassinating Japanese nobles inside their home, sneaking along rafters, killing rival ninjas. Important components include managing your prey's fear level, tracking via scent (colored trails ala Twilight Princess), and following your master's teachings in your new form. You never revert to your human form, but you do see your daughter off to a safe and happy life.