Aria was the Empress of Maple World before Cygnus. However, she was later killed by Lotus, one of Black Mage's Commanders. Following her death, the throne was given up to Cygnus, the niece of Aria, as Aria had no children.
Predicting that the Black Mage will be revived soon, Cygnus formed the Cygnus Knights to act as an opposing force against him. After Black Mage has been resurrected, Cygnus arranges for a meeting to take place in Ereve to create the Maple World Alliance. After Mercedes had awoken, Cygnus sent a few knights to protect Elluel in case of any incoming threats from the Black Wings.
During a meeting in Ereve, Hilla, one of the Black Mage's Commanders, disguises herself as an Empress, hoping to fool everyone into thinking that she is the real Empress of the Maple World. Using a Skaia as proof, a legendary jewel said to glow in the hands of the Empress, she nearly succeeds until Phantom shows up. He destroys the fake Skaia and reveals he had the real one all along. Hilla flees, and the real Skaia returns to its rightful owner, Cygnus.
Sometime in the relatively recent past, Ereve is invaded by Eleanor, who uses a curse that petrifies all its residents, including Cygnus. One unnamed Knight (who is portrayed by the player in the third Grand Athenaeum scenario) is not present due to completing a rescue mission, and arrives in the aftermath of the battle. Eleanor mocks him/her, even gloating about her plans to use Cygnus as a trophy, but she is defeated and Cygnus is revived.
During Black Heaven (Blockbuster), Cygnus is one of two most influential leaders of the Alliance, along with Claudine, but disagreements between the two - and outright arguments - happen frequently, especially where Orchid is concerned. Claudine demands harsh punishment, while Cygnus pleads for forgiveness. Another rift occurs when Cygnus defends the player after Claudine blames him for Francis' escape.
At the end of Black Heaven, Cygnus uses the final Seal Stone to heal the player. This has the unfortunate effect of making the Black Mage's freedom complete.
In the near future, Empress Cygnus became interested in the World Tree, the Transcendent of Life. The World Tree is said to grant immense powers, and Cygnus wishes to use this power against the Black Mage. Neinheart, however, advised against doing so. Eventually, Cygnus and her knights went to search for the World Tree. They succeeded, but fell into a trap laid by the Black Mage. Cygnus and her knights became corrupted and the island of Ereve is no longer held up by the magic created by Cygnus, and descended to Victoria Island. There, Empress Cygnus and her knights started to attack Henesys, although what happened to the rest of the world is unknown.
However, present day Shinsoo said that it was simply a facade caused by the Dream Stones, created by the Black Mage. Therefore, it is very unlikely that the Cygnus Knights will be corrupted by the Black Mage when visiting the World Tree and crash Ereve on Henesys.
When Damien kills Shinsoo and revived by Cygnus after awakening her powers, he leaves Ereve. When found by the player during a quest, he says that his duty was to make sure that Cygnus's descendent became the fourth Transcendent. Due to her awakening however, she instead is becoming the fourth, and will soon be a danger to herself and everyone. He left so that he could find a way to repress her new powers and keep Cygnus safe.
In FriendStory, Cygnus' counterpart is the sheltered, isolated, and incredibly lonely heiress of Shinsoo. She is drawn to the player quickly, who is very surprised that she is more out of place in Seoul than he/she is. Her philanthropic attitude towards the students, while well meaning, is viewed as naïve at times, both by the player and Neinheart.
- Cygnus is named after the Cygnus Constellation.
- Cygnus and her Knights were among the first Bosses to receive voiceovers.