Set in 2142, Wonderful Days depicts a world that has been nearly destroyed by environmental pollution. Human life as we know it is almost extinct, and only a few were able to pull through the collapse of Earth's ecosystem. In order to deal with the chaos, a city named Ecoban was created. The city uses the very pollution that caused the disaster as an energy source.

However, although the initial plan was successful to an extent, it didn't just create a new source of energy, but also an elite group of people. This prestigious faction believes that they are above the system, and are not willing to accept survivors from outside the city unless they are put to work as laborers.

Among the people living in the wasteland outside Ecoban is a young man named Shua. He leads a very difficult life, but tries to make the most of it through the love that he feels for his childhood friend Jay. Unfortunately, Jay may be more interested in her security commander Cade than in Shua, and thus a love triangle is formed. Not only does Shua have to deal with the heartbreak, but he must also find a new way to survive in the crumbles left from the once-beautiful planet Earth.