The son of Shamardal was sent off the second favourite behind odds on shot Erik The Red. Graham Lee settled Natural Nine on Erik The Red's girth and he travelled sweetly.
The leader tried to kick off the final bend but Graham had that move covered and urged Natural Nine into the lead.
He struck the front with a furlong to run and was pushed out to win by half a length.
Roger said: "He had a few near misses last year but did nothing wrong and it is great to get his head in front.
"He is suited by fast ground and will stay a mile."