Shift into the hardest/smallest gear on the rear cassette. This makes it easier to remove/install the rear wheel. Remove the front and rear wheels and replace the axles.
Partially deflate both tires and place the wheels in the bike bag. If you have tubeless tires, don’t deflate the tires all the way or you risk breaking the bead off the rim and losing sealant.
Place the hard plastic cover over the wheels and the soft padding on top.
Drop-bar bike: loosen the stem bolts, turn the handlebar 90 degrees, then rotate the bar to hook it under the top tube. Flat-bar bike: remove the bar from the stem and fasten it vertically to the stem and fork. Remember to put the stem cap back into the bike, so you don't leave it behind.
Mark the seatpost to the current height, loosen the seat post collar and take off the seat post.
Remove the pedals. If you have pedal washers, make sure you keep them in a baggie or zip-tie them to the cranks.
Partially deflate your front/rear shocks if applicable.
Place the frame and seat post in the bag and secure it with straps.
Your multitool and pedals can be stored inside the water bottles attached to the frame so that they do not rattle inside the bag.
Place the second soft padding on top of the frame and close the bag.