I was 8 years old when Nixon resigned, so I remember very little of it. I'd always assumed he resigned for altruistic reasons and so that the country could move on after he left office.
But I also wonder - did the Commission (or some other part of the government) have some type of damaging evidence that could have led to something catastrophic, and they agreed to bury it in exchange for his resignation?
On July 27, 1974 the House committee voted to impeach Nixon on three counts. Nixon was told by House and Senate leaders, the full House would vote to impeach and the Senate would find him guilty. Nixon resigned August 9. Nixon only resigned once he knew the Senate would remove him for office.
Nixon had recorded conversations in the oval office discussing Watergate and clearly guilty of obstruction of justice. The tapes Nixon recorded was the evidence that convinced his supporters in Congress Nixon must go. Conversations taken from the tapes were published by news media.
William F. Buckley Jr, wrote in 1984 for the NYTimes discussing the events in the link below. If there was a secret deal with the Watergate Commission Buckley would have known or suspected and wrote about the arrangement.