It looks very much as though Sir Thomas Perrot, MP was the only child of Sir John Perrot and his first wife Anne Chene(y). That Thomas was born in 1553 and Anne died in 1553 has...ominous implications.
Sir John took a widow, Jane Prust widow of Lewis Pollard, to be his second wife. The date of the marriage is uncertain, but was sometime before 1566. Sir John's second son, William, was certainly hers, and his shadowy third son, John Perrot II, may have been also. (If so, this would explain why Sir John didn't have to scramble to provide for John II the way he did James - John II was already in the line of succession.) But he was soon left a widower for the second time, as Jane died in 1568. (Incidentally, Jane's "birth" date of "1517" seems to be much too early. She cannot have been born to a father who was only four years old.)
Exactly when Sir John took up with Sybil Jones is unknown, but she did give him his fourth son, (Sir) James Perrot, circa 1570. Sir John loved him well enough to acknowledge him and make repeated efforts to insert him into the succession as a backup - in which he was not entirely successful, as later events showed.
Which daughters were Jane's and which Sybil's is also unclear (any born after 1568 would *have* to be Sybil's, or perhaps another mistress').
William, the second son (and first by the second wife), is reported to have died in 1587, unmarried and without heirs.
As for John II, he is last heard of entering Gray's Inn in 1583, and if he did not succumb to the diseases bred by the filth of London, he was certainly dead by 1594 - and just as heirless as William.
It was in 1594 that Sir John's eldest son Thomas died, leaving a wife and a daughter (he had also had a son, who died young). This precipitated a legal wrangle over the Perrot inheritance between James Perrot, Sir Thomas' widow Dorothy and her new husband (Henry Percy, 9th earl of Northumberland), and a legitimate cousin, Thomas Perrot of London. This is what makes it obvious that John II *must* have been deceased by then - he nor any one claiming connection to him had any part in the case.
The short of it is that James managed to inherit most of his father's lands, but the case dragged on for twenty-five years before the last of it was resolved.
