Thatcher was close to a deal with Fulham in the new year following several break-ins at his house in the north.
The 29-year old said: "It was really unpleasant and shook us. The transfer window coincided with the break-ins, but I am not disappointed the move fell through.
"I have three years left on my contract at City and I would like to stay."
Thatcher has already discussed his future at the club with caretaker boss Stuart Pearce: "When Stuart Pearce took over, he asked me how I felt and I told him that I am happy here."
Ben Thatcher has been called up to John Toshack’s summer training camp squad to fly to