In Bad Ending #1 on Story of Eastern Wonderland, Reimu is feeling down because she wasn't strong enough. Cue Marisa—enemy only a little bit ago!—show up to try to make her feel better.
A meta example. A group of people from famous Touhou remix circles joined together to create this in celebration of ZUN's wedding.
Kokoro's ending in Hopeless Masquerade. After learning of emotions through battle, she takes up performing Noh at the Hakurei Shrine. This gives her identity through purpose, and at the end, she even smiles for the very first time. It also throws Reimu a bone by finally getting her visitors and profits.
In the final chapter of Oriental Sacred Place, Reimu finally discovers the Three Fairies' hiding place...and decides to befriend them. After years of pulling pranks on Reimu and Marisa and getting chased away by them, the Fairies realize they'd rather live together as friends than as enemies.