In November 1746 Marie Louise contracted smallpox which, in those days, was often a fatal disease.
During her convalescence, her family received a sympathy note from her first cousin, Charles Edward Stuart, also known as the Young Pretender. Having recovered, in August 1747, the couple met and Marie Louise passionately fell in love with this first cousin, who returned her feelings, and they began an affair.
In Louise's circles adultery was widely accepted so long as it was done discreetly. However, as neither Marie Louise nor her husband had been unfaithful before, her mother-in-law kept a very strict eye on her as her husband was with the French army in Holland and her servants had been ordered, by her mother-in-law, to guard her virtue. Marie Louise and Charles then resorted to secret midnight coach-rides; however, her mother-in-law had alerted the Paris police who reported what went on.
After a while, Marie Louise found herself pregnant and resorted to sleeping with her returned husband to make him believe he was the father, but this enraged the jealous Charles into creating a scene.
Yet Marie Louise's husband did nothing and gossip began to spread. In January 1748, confronted by her own father as well as her mother-in-law, Marie Louise was forced to write to Charles ending their affaire. Nevertheless, Charles was still allowed to visit her and her family in order to refute the gossip about their affair.
In despair, Marie Louise wrote more letters to Charles, threatening suicide if he didn't come to see her. He did so some three months later, again in a midnight assignation, but only to tell her he had a new mistress, Clementina Walkinshaw. Clementina later gave birth to Charlotte Stuart, Duchess of Albany, the only one of Charles' children to survive infancy.
On 28 July 1748, Marie Louise gave birth to a son, who was baptised Charles Godefroi Sophie Jules Marie de Rohan. It was her mother-in-law who wrote to Charles's father, 'Old Pretender', in Rome to tell of the news, but not that this child was his grandchild. Despite having been accepted as a member of the Rohan family, several genealogical books note the fact that the Rohans fail to mention this child again.