The Matriarch is the public face leadership of the Universal Church of Truth; the religion centered around Adam Warlock's evil future self the Magus that sets to conquering the universe in the future. As Magus is treated as a God, The Matriarch is the public leadership of the group that more people would actually get to see as Magus has to hang back to a degree to preserve his mystique.
Magus probably spotted her in a brothel ("a sinful establishment") and chose this woman of easy morals, but with an iron will and a razor-sharp mind. She was perfect for this role involving power and influence.
Her lust for power causes her to betray Magus to Adam Warlock in the hopes that she will take over as the Church leader. But the Magus is well aware of this, having once been Adam Warlock himself in the same position. He had placed her as Matriarch because he knew she would betray him, thus completing the circle of his creation. After getting his use out of her, Magus drops her into a deep pit. She dies from injuries sustained from the fall, but not before Warlock discovers her and hears her last confessions.
In her plans to get rid of Magus, she did not want to kill Warlock since it would be destroying the Universal Church of Truth. She resorted to an electronic brainwash instead and that is how Adam was driven mad.
The Return of the Church
Matriarch Aqwen heads the new Universal Church of Truth from their homeworld Sacrosanct. Using the faith of billions to power their ships, planets, and the new guardsmen of the Church, the Cardinals, she still continues to gain followers in the belief of Adam Warlock as the true god of the universe.Whenone of their Templeships is nearly destroyed by the Guardians of the Galaxy, she dispatches the Cardinals to find them. They successfully get a blood sample and learn that it was their god Adam Warlock that stood against them. But this creates a problem, for they believe that Adam is in a cocoon located in their main church.
The Matriarch is approached by Adam, who claims that he will lead them in the future. She grows impatient and demands the cocoon be opened. The contents are not shown. Later, when Warlock transformed into the Magus, he faked his death and returned to lead the Church once again. Under his orders, the Matriarch was to capture a creature from the Fault that happened to be contained within Moondragon.
The Matriarch was able to capture Moondragon and was planning to give birth to their 'Baby God,' which would then kill the billions of followers of the Church on the planet. This plot was foiled by the Guardians of the Galaxy who rescued Moondragon. But the Magus had managed to capture Phyla, Mantis, Major Victory, Gamora and Cosmo. When Phyla helped release them all, the Matriarch attacked them. After a formidable battle, she was knocked unconscious by Major Victory.
The Faction War
After the return and death of the Magus during the Thanos Imperative, a separatist faction of the Church breaks off calling themselves the Western Spiral Order. In order to reunite the Church under her authority, Aqwen creates a sect on Earth to facilitate the resurrection of the Magus called the Life Science Institute. When she is captured by the Annihilators, her thoughts reveal their plan to Cosmo.
The director of the Life Science Institute becomes the new Matriarch of the Church in the meantime.
Powers and Abilities
After her the Church returned to the timeline, the Matriarch is powered by the Church's Belief Fonts, which turns worshippers prayers into belief energy. With it, the Mattriarch is powered by her will and has been shown to be able to mental attacks as well as energy blasts.