Makoto finds it difficult to talk to Touko, mostly because of her antisocial nature and the fact that Touko can be very accusative. Touko has expressed dislike for Makoto, saying she disapproves of him, but sometimes thinks of him as reliable. Makoto and Touko survive the Killing School Life together, and become members of the Future Foundation (although Touko is not an official member).
After completing Danganronpa 1, a "School Mode" becomes available, in which the students are depicted in Hope's Peak Academy but no killing game occurs, allowing the player to socialise with all other students in a manner somewhat similar to a dating sim. Touko's route, when completed, is one of the few that is explicitly romantic.
As a bonus mode, this is non-canon. However, the relationship has been depicted as possible in a canonical game, so it is not entirely fanon. Furthermore, as Monokuma's opening monologue in the opening of Danganronpa:IF states, the world is filled with "Ifs", decision points that create worlds all of their own, however hypothetical. From this School Mode, and hence this ending, could be seen to be part of its own alternative canon.
The ship sailed as a result of their friendly interactions in their Free Time Events. Both surviving the killing game has also helped.
- Naegi/Fukawa tag on AO3
- Fukawa/Naegi (game) tag on FanFiction.Net
- Fukawa/Naegi (anime) tag on FanFiction.Net
- Makoto's relationship with Toko on Danganronpa Wiki
- Toko's relationship with Makoto on Danganronpa Wiki