Chop the tops and bottoms off the oranges, so a little bit of flesh is showing. Cut oranges into quarters and peel, working to peel away as much of the membrane as possible.
Put peels in a large pot of cold water and bring to a boil over medium-high heat. Boil for 10 minutes, Drain and cover with cold water again and boil for another 10 minutes. The peels will begin to soften.
Drain and run the peels under cold water, so they can be handled. Using a spoon, scrape all that white pith out from the inside of the peel. Chop the peel into thin strips.
Peel the remaining membrane off the oranges and put the fruit in a large pot. Squeeze the juice out of the membrane into the pot, too, before you discard it. Add the chopped peel and 2 cups of water. Bring to a boil over medium-high heat and then reduce heat and boil gently for about 30 mins. Peel should be very, very soft.
Remove the pot from the heat and pour mixture into a large heat-proof measuring cup. If you don't have 3 cups of fruit mixture, add more water to measuring cup until you do. If you have over 3 cups, discard anything over.
Put this mixture back into the pot stir in granulated sugar and chopped habanero pepper. Bring mixture to a boil over medium-high heat, stirring frequently.
Continue to boil, stirring constantly, until the mixture reaches the “gel stage" at about 220 degrees, which should take about 30 minutes. You’ll notice the mixture will be jelly-ish, but not totally solid. It will firm up once you put it in the fridge.
You can either can your marmalade (using proper canning technique) or you can simply put your marmalade in a clean jar and refrigerate.