Her brother succeeded his grandfather at age three and her uncle, Walter Scott of Goldielands, a natural half-brother of her father, led the Scott family during his minority. The feud with the Scott family was over but her life was not peaceful. In the year of her marriage an English army demolished the Kerr family seat of
Ferniehirst Castle. Her husband was involved helping
William Kirkcaldy of Grange who tried to hold
Edinburgh Castle in the name of Mary the exiled Queen during the
Marian Civil War and in 1573 he had to go into exile abroad. She and her husband were thought to have lent money to Grange against the security of the
jewels of Mary, Queen of Scots. When
Robert Melville was questioned about Mary's jewels, he said he did not know which pieces, if any, were held by Jean Scott, but her "great friend", Margaret Learmonth, Grange's wife, would know. In July 1575 he wrote from Paris to
Mary, Queen of Scots, describing the destruction of his houses with fire and gunpowder by English forces during the
Marian Civil War costing him at least 20,000 crowns, and the injuries sustained by his family and followers fighting for her cause in Scotland. He had lost his jewels and the charters of his lands left in a coffer in
Edinburgh Castle which
Regent Morton confiscated in 1573. The
Earl of Angus cut down his woodlands. In 1578, when one of the servants of Mary, Queen of Scots, in England,
Mademoiselle Rallay, was old and wished to retire, Mary thought of employing Janet Scott's young daughter in her place. Queen Elizabeth would not allow this. Probably, it was thought the girl might become another conduit for Mary's secret correspondence. Thomas Kerr, laird of Ferniehirst, returned to Scotland in 1581 but left again by 1583. Janet was given power of attorney over her husband's business affairs in Scotland and France and she ran them during the 1580s. In October 1583 she wrote to
Mary, Queen of Scots from Ferniehirst with news from the Scottish court. She said she had been approached by the
Countess of Arran in person and by letter hoping that Mary would not join with the Hamiltons against her husband
James Stewart, Earl of Arran. She wanted Mary to advise her about this. She had forgotten to forward a letter from
Lord Seton. Mary was a godparent to one of her sons. Lord Seton passed some of his letters to Lady Ferniehirst for her to address and forward to Mary, as he thought this would deflect suspicion. Mary had sent her a ring as a token. She received the queen's letter and the ring from her son, and she hoped to speak with the bearer of the letter who would have personal news from Mary. In February 1584 she hosted six Englishmen at Ferniehirst. Two of them, calling themselves Foljambe and Tunstead, were fugitives sent by Mary, Queen of Scots, who had arrived Scotland in January by "a very wild and dangerous passage", and they stayed in the tower for fear of being captured and returned to England. Two of Lady Ferniehirst's servants escorted the pair to
Seton Palace and they met the king at his hunting, and then went north to
Huntly Castle. The English ambassador
Robert Bowes heard that one man was really
Sir Thomas Gerard of
Bryn (who was involved in the
Babington Plot). The Laird of Ferniehirst made preparations for a border meeting in July 1585, and needing to have an ensign or flag made, used one of his wife's skirts. Lady Ferniehirst formed a good relationship with
Anne of Denmark. In December 1591 she persuaded her to intercede with
James VI to allow the exiled
Laird of Buccleuch to return to Scotland. ==Children==