A couple possibilities I see here.
* He runs for a fifth term. He was a member of NYC's Dutch/WASP establishment, and saw himself as a born ruler. He didn't want to give up power, which is demonstrated by the fact he ran for four terms.
* He lets Truman run in 1949. This would make especial sense if Roosevelt's health was poor like OTL.
* He screws up the war effort (i.e. doesn't bomb Japan and leads to a long and costly land invasion) and is impeached.
* He successfully completes his fourth term and then goes off to retire.
* He wins the war, and then retires, figuring he is no longer needed, and wants to spend time with his family.
* He wins the war, and is pushed out of office by Eisenhower and Truman.
* Other.