The defueling process is pretty slick. On a 688-class submarine, they remove a semi-cylindrical section of the hull around the reactor compartment (RC) before landing a temporary building on the RC.
One tricky bit is the fact that the spent fuel is so radioactive that it still makes a significant amount of heat. The thermal power is low enough that sinking it away from the fuel isn't difficult, but if such measures were not in place, the fuel would heat up until (redacted) Something Bad Happens. So every step along the way has either timing and/or heat sinking requirements involved.
One tricky bit is the fact that the spent fuel is so radioactive that it still makes a significant amount of heat. The thermal power is low enough that sinking it away from the fuel isn't difficult, but if such measures were not in place, the fuel would heat up until (redacted) Something Bad Happens. So every step along the way has either timing and/or heat sinking requirements involved.