Fortify my home, filling the bathtub with water and going upstairs with all my supplies, weapons, ammo, friends and family and checking that my secure getaway plan works properly before destroying the staircase and waiting it out.
What would you do if a ninja was charging you? Assume he's very fast and agile (he's a ninja, duh, but still. It was worth pointing out), he'll reach you in 5 seconds and he has a ninja-to.