The game drew praise from critics for its enigmatic, mature storyline and high production values, but was criticized for some of its more obscure puzzles.
This meant that the Balance is now unguarded, allowing Chaos from Arcadia to breach the Divide, explaining all those strange things happening in Stark. As Adrian is no longer in the Guardian’s Realm, the only way back there is through the original location where the Guardian’s Tower was built. He is also the only one who can open the entrance. Tobias reveals that April is a strong shifter. As April doesn’t know how to shift yet, she visits Brian Westhouse, a friend of Cortez and originally from Stark. There he gives her a pocket watch, which April uses to unintentionally open a shift. Back in Stark, Cortez fills her in with more information about the Vanguard, also known as the Church of Voltec. That night April ruins Zack’s date, establishing a vendetta with Zack.
The next day April visits Warren Hughes, a homeless boy with clandestine activities and connections. He agrees to help April if she infiltrates a police station to wipe his criminal record and find his sister. April does this, and also finds a data cube on the Church of Voltec. Hughes then refers her to Burns Flipper. Flipper then reads the data cube and finds out that Jacob McAllen, a Hitler-type person, is the head of the Vanguard. And Gordon Halloway, a cold ruthless person, is McAllen’s right hand man. Halloway was meant to be the next Guardian, but Vanguard experiments split him into two, Chaos (in Arcadia) and Logic (in Stark). He tells her that MTI (a very large multinational company) is the front of the Vanguard, and its HQ is located in Grendel Avenue, upper-level Newport. She needs a fake ID, which Flipper will make, to access the upper levels.
Meeting Cortez and Father Raul in a Christian cathedral, Cortez tells April that Arcadia is on the brink of war. Still waiting on fake ID, she goes back to the Border house for the night. She then unintentionally shifts back to Arcadia. Entering The Journey Man inn, she meets the innkeeper Benrime Salmin. Also there is a strange creature, Abnaxus, ambassador of the Venar who happens to know who April is. His species sees all of time, but there is a dark veil in the future that he cannot see past. That is the time of uncertainty and chaos. After he leaves, April falls asleep in a chair in the inn.
In the morning, she visits the great Library of the Sentinel Enclave. She learns there are four magical species that guard the parts of the disc, and each has prophecies of a savior who will restore the balance, only to finally break it. She gets a lead, the island of Alais, where flying creatures called the Alatian have tales since the start of the Divide. She gains passage on a ship that will take her to Alais, The White Dragon. She does this by rescuing a talking bird that she named Crow. However before she can leave, she has to first free the wind, which an evil Alchemist, Roper Klacks, has put a spell on. Leaving for Klacks Tower, Crow escapes from his drunken owner and joins April on her journey.
On the way to the tower, she gets captured by an evil woman, the Gribbler, in the forest. The Gribbler eats humans and furry creatures called the Banda. April kills the Gribbler, while rescuing one of the captive Banda. The Banda honor her for saving their species and give her accommodation for the night. That night, she gets visited by their spirits who gives her the name April Bandu-embata. This then fulfills the prophecies of the Banda, and they give her the first piece of the disc.
When April arrives at the tower, she finds herself in a labyrinth. After much searching, she finally finds Klacks. She challenges him to a maths duel: his magic versus her calculator. He loses and snatches the calculator from her. He is intrigued with the device to the point of insanity then gets sucked in it. With Klacks' magic, April manages to free the wind. Just before April sets sail for Alais, Tobias tells her that she is the next Guardian, and gives her the Talisman of the Balance. April is shocked with this news, especially because Tobias kept this from her until now.
On the voyage to Alais, a Chaos Storm attacks the ship. The captain changes course, but with the fate of the Balance in peril, April sabotages their compass with her talisman to resume course. In the middle of the storm, April wants to retrieve the talisman, but is noticed by the captain. He realizes what she has done and prompty locks her Talisman in the deck down below. April tries to retrieve the talisman, which is locked in a chest, with an axe, but ends up sinking the boat.
She wakes up on a wooden debris raft, with only Crow to be found nearby. The rest of the crew had been rescued, but left her to drown as punishment for sabotaging the compass. Just after Crow leaves to search for land, April gets pulled down to the bottom of the ocean by the Maerum (Mermaid-like creatures). Initially there to serve them as a fishing slave, she meets the Maerum queen, recovers her Talisman and uncovers an ancient cave showing the history of the Maerum and Alatian (who are both enemies). The two species are revealed to have the same ancestors and have lived in peace for many years before the war. They used to live together with no problems at all, however now food has become scarce as they both left their initial territory. April shows the Maerum her discovery, which happens to fulfill one of the prophecies of the Waterstiller, some sort of savior for the Maerum. After fulfilling the second prophecy, killing a dangerous Snapjaw, only one prophecy remains: for her to reunite the Maerum and the Alatian. As such, the Maerum take her to Alais.
After searching through ancient ruins, going through large forests and climbing up in trees, she finally arrives at the Alatian village. Learning the four important tales of the Alatian, she manages to get an audience with the Alatian Teller, who is as a Queen her people. She fulfills the prophecies of the Windbringer by flying without wings (with the help of a little magic) and convinces the Alatian Teller to try to make peace with the Maerum. In an abandoned coastal sea cave where both species once lived together, ambassadors from each side (the Teller's guard and the Maerum Queen) brings stones which combine to from the second part of the disc. April then asks the Maerum to take her to their sleeping God. There she meets the Blue Dragon, who gives April one of the Jewels which are to fit into the disc. The Blue then takes her to a ship inhabited by the Dark People, which had set sail for the specific purpose of giving April the third piece of the disc. The Dark People had also searched through their extensive library to locate the position of the Guardian’s Realm entrance. It is revealed to be space and they give her a star map with its location.
Back in Marcuria, the city is abandoned and on the edge of a Tyren invasion. At the Harbor she gets attacked once more by the Chaos Vortex, now even bigger than before. Petrified, she accidentally opens up a shift behind her leading to the Cathedral in Stark. Father Raul reveals he is a Sentinel Minstrum of Stark, and tells her that Cortez has gone missing. April then goes back to the Borderhouse, where Gordon Halloway is waiting for her. Zack has sold April out as revenge for standing him up. April manages to escape, but Emma and Zack get shot as bystanders. April heads for the Fringe Café but Halloway's assistants quickly catch up with her.
Miraculously, a shift appears that leads to a wooden cottage with Lady Alvane. Alvane had opened the shift for her, and tells April she is in neither Arcadia, nor Stark, nor the Guardian’s Realm. She reveals that the Vanguard are holding Adrian captive, and teaches April how to shift at will. Alvane sends April back where she visits Abnaxus, who was expecting her, the Kan-ang-la. His people have been guarding the fourth and final piece of the disc, which he gives to her. At the Enclave, April learns that Tobias has been murdered. There, she unites the four pieces of the disc into one. With the Tyren army having just arrived at Marcuria, the road back to the city is blocked.
April then finally opens a shift by herself and arrives back to the location of the White Kin. The White is dying, with her fight against Chaos taking its toll. She gives April her jewel, reveals herself as April's actual mother, and then dies. April is understandably shocked, not realising that her childhood adoption was quite so significant. The White's egg then hatches a new White Kin, April's 'sister'.
Shifting back to Stark, April gives Flipper the star map for him to decipher. Receiving the fake ID, she goes up to Grendel Avenue. Whilst digging through McAllen’s office, she triggers an alarm and McAllen traps her in the room. He tells her he has Cortez captured, and has the two Stark jewels of the Kin. He plans to place Halloway in the Tower, and reveals the Chaos Vortex is the Arcadian half of Halloway.
Unable to shift out of the building due to magical barriers McAllen had installed, she surrenders the 2 jewels and the disc, which he then stores in a safe. Refusing to tell him where the Guardian’s entrance is, McAllen leaves April alone in room containing a machine that breeds Warrior Shifters. One of them manages to break free and attacks April. She manages to escape out onto a hoverpad high above the city, but is once again trapped. Cortez then appears in the nick of time, having escaped, and kills the monster. McAllen then appears confronting Cortez. It is revealed that they both are the two Stark Kin. Also revealed is that McAllen had created the Vanguard and wanted accelerated reunification so the Kin could be free of humankind, even if this meant an age of Chaos. The two Kin then attack each other but and end up falling off the pad into the city. They transform from their human form into dragons, but it appears they both die.
Retrieving the disc and the 4 jewels, April returns to Flipper. He had attempted to sell April out to Halloway, but had been mortally wounded as 'payment'. Halloway took the deciphered map, but Flipper had managed to make a copy, which he gives to April before dying. The entrance to the Guardian's Realm is near the 'Morning Star', the busiest space station in orbit around Earth, and Halloway was apparently taking Adrian there. At the station, April locates and frees Adrian. Launching themselves from the station in separate maintenance pods, they approach the correct co-ordinates, and Adrian opens up a massive portal. They both enter, and Halloway sneaks in behind them just before the portal closes.
In the Guardian's Realm, April crash-lands alone. Before she can reach the Tower, she must complete 3 trials. On her way to the tower, she encounters the Chaos Vortex once more, this time sealing it into her Talisman. After the first two trials, she manages to summon Crow through a small portal. He then helps her complete the third task but goes missing, so April continues forward. Adrian then appears and lets April inside the Tower. Inside, it is revealed that April is not the next Guardian, but Halloway, who just enters, is. April then reunites Halloway with his other half which was in her Talisman, making him balanced. As April’s job is now complete, she leaves Adrian and Halloway to complete the changing of the guards. Uncertain of her future, April, whose life has completely changed, continues her journey back to the 2 worlds. Crow finally returns to find that April has left.
In the Epilogue, the scene returns to Lady Alvane’s home. She has finished telling April’s story to two teenagers, who look like they are from Arcadia. She reveals that Halloway was the last Guardian and during his reign the two worlds were reunited. When the children leave, Crow enters who is clearly well accustomed with Alvane. They have had a long life together with many great adventures, raising the suspicion that Alvane could be April in the future. He also asks Lady Alvane to recount the tale of the young beautiful "warrior princess" who single-handedly won the war of the balance. Alvane remarks she doesn't remember it quite like that, but the story begins a long time ago, when Stark and Arcadia were still to be united, and the Guardian was still on his throne. It is possible this is a reference to the sequel, Dreamfall.
Note: the actor names above are for the English language version.