When you land on the other side of the "portal", return back to Crysta. The villagers are glad to see you when you talk to them, but then a voice is heard commenting that if you had never found out the truth, you would of been happy. The villagers then begin to turn into spirits and attack you.
Return back to the Elder's house. Walk back to his room and speak with him. The Elder says that you've learned more then you should have. He then says he wants to show you something. Follow him back outside the house and talk to him again. Elder says that all the humans here are replicas made by the same material. When the human replica's use up their energy, they convert back to their original form, which just happens to be the Crystal Blue that floats through the sky! He also explains that the world has two sides; the Light Side that creates life and the Dark Side that destroys what isn't necessary. The Dark Side has now willed that Ark is no longer necessary! The two of you then turn into spirits and teleport to the Gaia Stone.
Ark rematerializes on a long endless path. Spirits are floating and disappearing around him. A voice is heard saying that this is the Gaia Stone, which is located in the center of the underworld's sun. The voice explains that the Light is creation and Dark is destruction and the two will soon become one.
Dark Gaia will also fly around over your head where you cant reach him. You have to hit his body in order to damage him. When he gets close enough hit him with your HeroPike to eventually destroy him.
After Dark Gaia is destroyed you're left alone on the platform. A voice is heard that sounds very familiar. In fact, it's the same voice Ark heard when he was placing the StarStones at the South Pole. The voice is glad that you have resealed Dark Gaia's power. Ark asks who he is, and he explains that he's the Ark of the Light Side! Dark Gaia had created a copy of him and of his home town of Storkolm when Dark Gaia was originally sealed away. The copy that was created was Ark and Crysta! Ark of the Light Side says that your work is done and teleports you back to Crysta.
Of course with the destruction of Dark Gaia, there is no one left in Crysta. Ark becomes saddened because everyone is gone, and remembers how Princess Elle also lost her entire village. Yomi pops out of his box and inquires as to why he is so sad. Ark wonders what he has been fighting for the whole time. He followed the Elder's orders to resurrect the world but believes that he also brought bad luck to the planet.
Yomi is surprised to hear that Ark has such a sense of duty even though he fulfilled it by resurrecting the world. The humans would consider his actions god-like, and where there are living beings bad things are expected to happen. Yomi says that there are just as many good things that happen as well.
Ark finally asks what Yomi what he actually is. Yomi explains that all living beings evolved out of one single creature and that all living beings looked like him at one point in time. Yomi finds humor in the idea that one day humans may evolve back into what he looks like. Then he says he has to return back to sleep until the next time he's needed.
Yomi disappears. Four spirits appear and surround Ark. Light Gaia speaks and explains it's the soul of the surface world. Now that Dark Gaia has been destroyed, Crysta and the rest of the underworld will soon disappear and the surface world will return to normal. Ark is the hero that appears when the world is in danger and has both Light Gaia and Dark Gaia blood flowing through him. Soon Ark too will also disappear. Light Gaia says spend your last happy day in Crysta.
Ark is then transported back into Elle's room at the weaver's house, but Elle's alive again! She says you were standing there zoned out for a second. The rest of the inhabitants are all so very happy. The shops have never heard of MagiRocks and Ark's friends have never heard of an Elder. They say the blue door in the Elder's house has always been a broom closet.
When Ark is finished, go to his bedroom and crawl into bed. Ark will fall asleep and dream of Elle. She explains that she tried to destroy Ark when he was a baby because the Elder's word was final. She finally realized that everyone are individuals and need to live naturally. Elle says that Crysta may be gone, but she will meet Ark again. She then says goodbye and fades away. Ark then starts to dream his last dream; he's a bird and fly's all over the world, watching it get older.....