Morrison Foster saw Stephen often during these years, and he tried hard to straighten him out. He gave him clothing, which Stephen usually sold for a few dollars as soon as Morrison had left. When Morrison told Stephen that he'd be afraid of being insulted if he himself were dressed so shabbily, Stephen replied: "Don't worry, Mitty. No gentleman will insult me, and no other can." Morrison was living in Cleveland he tried to persuade Stephen to go there with him. But Stephen stayed in New York. He had friends there who would try to reform him, and he was still the lovable and generous Stephen he had always been. Morrison was quite accurate when he said that the drink habit was the only failing Stephen ever had.

In January of 1864, he was living in a lodging house at the corner of Bayard Street and the Bowery, then known as North American Hotel. He was ill and suffering from a "fever and ague." He may have been tuberculous; several of the Fosters are known to have had the disease. On the morning of January 10th, George Cooper received a message to come quickly to the hotel. Stephen was lying on the floor of his room. He had risen from his bed and fallen on a piece of crockery. Along his neck, near the jugular vein, was a long, bloody cut. A doctor came and sewed he cut with black thread. Then they dressed Stephen and took him to Bellevue Hospital.

Cooper wrote Morrison, and asked him to send money. Stephen improved at first, but on the third day in the hospital he fainted while his wounds were being dressed, and never became conscious again. He died at half past two on the afternoon of Wednesday, January 13, 1864. Cooper sent Morrison a telegram which arrived ahead of his letter. So Morrison and Jan, joined by brother Henry, came to New York and took Stephen's body from the morgue, back to Pittsburgh, where it was laid to rest in the family plot in Allegheny Cemetery.