In earlier poems Morgaine the Fay is not shown to be evil, but has her own agenda, which may not always be compatible with Arthur’s, After all, she is a fay, although sometimes also identified as Arthur's half-sister or step-sister.
According to the “Prose Lancelot" (and the English poem “Sir Gawain and the Green Knight”), Morgaine did have a dislike of Guenevere. Morgaine had earlier lived in court and had an affair with Guyomar, a nephew of Guenevere. Guenevere found them sleeping together and declared that unless this stopped at once, she would tell Arthur that Guyomar was fooling around with Arthur's sister. Guyomar feared for his life and immediately gave up Morgaine. Morgaine, in anger, went off to Merlin where she learned magic. When Morgaine discovered that Guenevere and Lancelot were having an affair, she attempted to take vengeance by revealing it, but Arthur would never believe her, especially as events tended to confound what Morgaine claimed.
The story of Guyomar may be an adaptation of any earlier story in which a knight named Guigomar was Morgaine’s secret lover, but she left him when he revealed the affair to Guenevere when Guenevere attempted to vamp him. Eventually, when Guigomar was at point of being put to death in a trail for insulting Guenever, Morgaine came back and rescued him. Guigomar/Guoymar is probably in origin the same as Sir Gringamore or the Isle of Avalon in Malory’s story of Sir Gareth in his “Le Morte d'Arthur”.
In later romances Morgaine, as an enemy of Guenevere and Lancelot and a notorious seductress of knights, is sometimes blackened further in character, and made an enemy of Arthur himself. In the so-called “Post-Vulgate Merlin”, we have the story of how Morgaine attempted to take over Arthur’s kingdom and to slay her own husband King Urien with the aid of her lover Accolon. This story passes into Sir Thomas Malory’s “Le Morte d'Arthur".
Note that this is almost the only Arthurian tale in which Morgaine is married to Urien. In other tales she is not married to Urien and is not the mother of Yvain/Uwaine the son of King Urien. There was a Welsh tale that Owein son of Urien was the son of an encounter between Urien and the fairy daughter of the King of Annwn and this seems to have been adapted by some French writers.
But the story that Morgaine rescued Arthur in the end still remains.
Note that the tale that Mordred was a son of Morgaine and that Morgaine was one of the plotters of Arthur’s final battle is pure invention of modern novelists who tend to copy one another rather than bother with the actual medieval stories.