The Queen dowager married her old flame, the Lord Admiral, Thomas Seymour, brother of Edward Seymour, the King's Uncle and Lord Protector of England after the king's death. Elizabeth went to live with the Queen and her new husband, and a new era of trouble began for her. Thomas Seymour, a dashing man in his late thirties, took an unhealthy interest in his new step-daughter, who had just turned fourteen. Seymour's interest in Elizabeth was blatantly sexual, and neither Katherine, Kat Ashley, or Elizabeth herself was comfortable with his behaviour. Matters came to a head when Elizabeth was reputedly found alone with the Admiral, and Katherine, concerned and perhaps a little jealous of his attention in the young girl, thought it would be better for her to leave the household. Elizabeth accordingly left, although there was no enmity between the two women. The Queen soon gave birth to a daughter, who was named Mary, but Katherine did not survive the birth.
Leaving the household was not the end of Elizabeth's troubles with the Admiral. Shortly after his wife's death, Seymour began to seek Elizabeth's hand in marriage. Elizabeth turned him down. Seymour was jealous of the influence his brother had in the country and over the boy king, and he planned a coup to give himself that power. He planned to abduct the king, marry him to Lady Jane Grey, and marry himself to Elizabeth. His plans failed, and he was arrested for treason. His plan to marry Elizabeth implicated her in the plot. It was high treason for an heir to the throne to marry without the consent of the Monarch, Privy Council and Parliament, and Elizabeth stood in great danger from those who felt that she was complicent in his marital schemes. She was also subjected to a rigorous questioning on her relations with the Admiral by Sir Robert Tyrwhit. She was only fifteen years old, but one careless word from her could have sealed the fate of all those who were dear to her, and possibly have cost her her own life. In such difficult and frightening circumstances, and with virtually no assistance, Elizabeth managed to uphold her innocence. The Admiral, however, was found guilty of high treason and condemned to death. The effect of all these on Elizabeth had been immense and it took it's toll emotionally and physically. However, as well as effecting her health, it also affected her reputation. Elizabeth was always very sensitive about what people thought of her, and she wanted the rumour that she was pregnant by the Admiral suppressed. She wrote to the Protector asking for a proclamation to be made saying these things were false. Although this was considered, it was not implemented. During the investigation, Elizabeth had been parted from her governess, and it was sometime before they were reunited.
In these troubled years, Elizabeth's relationship with her brother suffered. They were no longer as close as they had been, and during and immediately after the Seymour scandal, Elizabeth was forbidden to attend court. She was eventually allowed to return. To try and recapture her virginal image, Elizabeth dressed as the perfect Protestant lady. She wore plain black and white gowns, refused to decorate herself with jewellery and other finery, and refused to wear make up. Her sobriety was much commented upon, and even her brother called her "sweet sister temperance".
Following the disgrace and death of his brother, Thomas, Edward Seymour was replaced as Protector by John Dudley, Earl of Warwick, soon to be the Duke of Northumberland. He was the father of Elizabeth's childhood friend, Robert Dudley, and they may have seen each other a number of times during the Duke's government. Edward had enjoyed a rather healthy childhood, but from 1553 onwards, be began to be very ill with possibly a form of consumption (TB). It became clear to Northumberland that the young boy was not likely to survive into adulthood, and he thus had to make preparations for the succession. The heir in English law was Edward's sister, Mary, but she was an ardent Catholic, and her accession would undoubtedly put an end to Northumberland's reforms of the church, and his personal power. To prevent a Catholic succession, Northumberland devised a scheme that would both preserve Protestantism, and his own influence. If both Mary and Elizabeth were excluded from the succession, then the crown fell on either the Stuart line through Henry's oldest sister Margaret, or the Suffolk/Grey line through his younger sister, Mary. Henry VIII had excluded from his will the claims of the Stuart line, and so the crown would fall directly on Frances, Duchess of Suffolk. Both Mary and Elizabeth were again bastardized, and excluded from the succession, and Frances was set aside in favour of her daughter, Lady Jane Grey. Northumberland had further married his youngest son, Guildford Dudley, to Jane, thus ensuring the influence of the Dudleys. Three days after Edward died, on 6 July 1553, Lady Jane Grey was proclaimed Queen. The coup failed as Mary put up a strong and successful fight for her throne, and gained the overwhelming support of the English nation. She was proclaimed Queen on the 19 of July in the capital, and five days later, Northumberland was arrested, and later executed. Mary triumphantly entered London amidst the cheers of the people, and Elizabeth was given the privileged of riding with her.