The Franco-Spanish war had been continuing in north Italy, and late in 1654, increasing Piedmontese hostility to the current French commander Grancey led to a search for a new allied commander-in-chief; the French would have preferred to send the Duke of York (later King James II), but he too was unacceptable to Turin, so Thomas was appointed as joint commander - though his wife was held in France almost as a hostage for his good behaviour. On 16 December 1654 he arrived in Turin, to a ceremonial welcome by the French troops and an unexpectedly friendly reception by Charles Emmanuel. On 4 April 1655 Thomas Francis commanded the Waldensians to attend Mass or remove to the upper valleys, giving them twenty days in which to sell their lands. The Duke of Savoy sent an army and on 24 April, at 4 a.m., the signal was given for a general massacre so brutal, that it aroused indignation throughout Europe. Oliver Cromwell began petitioning on behalf of the Vaudois, and John Milton wrote his famous poem about this, "On the Late Massacre in Piedmont." In the 1655 campaign, he led an invasion of the Duchy of Milan, though already ill with malaria, and besieged Pavia, where the attack went so badly that he was forced to leave his sick-bed to take direct control of the siege, and even then it had to be raised after nearly two months of fruitless effort.