Preparations for the second trip to Yucatan were well underway on September 24th, 1841, when Stephens wrote his friend Prescott, "You would oblige us... by not mentioning our purpose. We wish to get off without any newspaper flourishes and without directing attention at all to our movements."
Stephens and Catherwood sailed from New York on October 9th, 1841. They were joined on this voyage by Dr. Samuel Cabot, of Boston, a surgeon and accomplished amateur ornitholigist, of whom Stephens would write, "we are glad that he is with us." On October 27th, as the bark Tennessee lay at anchor off the coast of Sisal, the port city of Merida, awaiting customs clearance, Stephens wrote to his father, "What awaits us... remains to be seen, though I am not quite so confident as when I had a diplomatic commission.... It is provoking to be anchored three miles off this vile little place and not be permitted to go on shore...."