Although the park service is exploring options which might offer a compromise, when staying on Isle Royale you need to choose between cost and comfort: sleep in your own bag outside for free, or sleep in a bed indoors and pay the expense of civilized amenities in the wilderness.
backcountry
True backcountry camping – hiking off the trails and camping in non-designated sites – is allowed only with a special "cross-country" camping permit. It's advised only for experienced wilderness hikers due to the frequent ruggedness of the terrain and difficulty navigating in mostly-wooded areas.
camping
The vast majority of visitors to Isle Royale stay in the designated campgrounds maintained by the park service, equivalent to what most parks call "backcountry" camping... nothing like the half-paved communal parking lots usually passed off as "campgrounds". Some are accessible only through the network of trails crossing the island, some are accessible only by water routes, but many can be reached either way. The motorboat-accessible campgrounds may not be ideal for hikers and paddlers trying to get away from civilization. There's no charge for campgrounds beyond the park visitor fee.
The only amenities at these campgrounds are enclosed pit toilets... no electricity, showers, or trash cans. Campgrounds on the shore of Lake Superior usually have picnic tables; inland campgrounds instead have a some large local logs to sit on. Most campgrounds have several fairly isolated "individual" sites, clearings big enough for two 1-to-3-person tents. Shoreline campgrounds usually also have a small number of three-sided, covered and floored wooden shelters the fourth wall is screened, but these can't be reserved, so you need to bring a weatherproof three-season tent or risk spending the night with no protection from the clouds of rain and mosquitoes. For that matter, the tent sites can't be reserved either, so during times of heavy use, you might have to share an individual site with another party. Some campgrounds have larger tent sites for groups of 7-10 campers located away from the "regular" sites, to reduce the disturbances such groups produce which must be reserved. Most campgrounds have a three-night limit on how long you may stay, and the most in-demand ones have shorter limits.
The park's campgrounds, from one end to the other: numbers correspond to locations on map
Rock Harbor Lodge
The only option for those wanting a bed and four walls, the lodge offers both modest modern hotel rooms overlooking Rock Harbor/Lake Superior, and modern duplex "housekeeping" cabins inland with nice big picture-window views of the surrounding trees, all a short stroll from the dock.