Toilet flooring and sub flooring rotten
You will have to remove the toilet to determine what you'll need to do to repair the floor. The hardwood flooring is probably going to make it a little more difficult.
The tools that you will likely need will be a measuring tape, a framing square, an adjustable wrench, a flathead screwdriver, a circular saw with old blade (you WILL hit nails), a drill motor with Phillips head driver for screws, crowbar, flatbar, hammer, chisel, safety glasses, and gloves.
The materials that you will probably need will be a new wax ring seal and set of (2) brass toilet bolts, a 2' X 2' piece of 3/4" pressure-treated plywood (subflooring), a 2' X 2' piece of 30 lb roofing felt, a pressure-treated 2" X 8" X 8' board (floor joist), Liquid Nails, 1.5" sheetrock screws, and whatever hardwood and hardwood nails that will be required.
Removing a toilet:
Turn the water off (hopefully the toilet has its own shut-off, or now is a great time to install one).
Flush the toilet and sponge out the leftover water in the tank and bowl. Disconnect the fill tube.
Loosen the two toilet base bolts and tip the toilet over onto a pile of old carpet or towels out of the way. Stuff a rag in the toilet drain to prevent sewer gas.
Cutting out the floor:
Adjust the circular saw blade depth so that it only cuts the flooring depth and NOT into the floor joists. Cut out the damaged wood back to the center of the next undamaged floor joists.
If the top of the floor joists are damaged, sister a piece of the pressure-treated 2X8 onto them level with the top of the joists. Install crosspieces of 2X8 half under the old flooring between the joists.
Measure your subfloor plywood, cut it to fit the opening, then cut it in half to fit around the drain pipe hole, put Liquid Nails on the top of the joists and crosspieces, and screw the subflooring down. Staple the roofing felt on top of the subflooring (for a vapor barrier if the bathroom is over an unheated basement or crawlspace).
Proceed with fitting the hardwood. Without being able to see anything, this should get you started.
We'll be glad to help you from here.