Oklahoma doesn't publish their vital record dates, not even a death index. Of course this makes finding where and when someone died more difficult especially with a surname of Jones.
Thomas Denton Jones, b. 12 June 1848, Tennessee
Died: 1909, Vian, Sequoyah, Oklahoma
Source: Az's Winding Roots family tree, ancestry.com. Most larger libraries provide free access to Ancestry.com if you have a library card.
I found the following:
1900 Calf Creek, Searcy, Arkansas
Thomas D. Jones, b. GA June 1848, marr 23 yrs, farmer
Mary E., wife, b. AR Feb 1860, had given birth to 10 children but only eight alive in 1900
Elizabeth, b. MO June 1879
Amous, b. MO Nov 1882
Alburt, b. MO, April 1885
Ulis Grant, b. MO, April 1887
Arty Mandy, dau, b. MO March 1889
Molly M., b. MO June 1871
Sarah O., b. MO Dec 1893
Miney M., dau, b. AR Nov 1894
1910 Mckey, Sequoyah, OK
Mary Jones, widow, b. AR, 47, farm laborer working out
Mollie, b. MO, 18, farm laborer working out
Leta, b. MO 17, farm laborer working out
Minnie, b. MO, 16, farm laborer working out
Lizzie Hefner, dau, b. MO, 21, had given birth to four children but only three alive in 1910
Freddie hefner, grandson, b. AR, 7
Gertie Hefner, granddau, b. AR, 3
Babe Hefner, grandson, b. MO, 4/12ths
It looks like Thomas could have died in Arkansas, Missouri or Oklahoma based on where his children were born.
I looked through the cemeteries and obituaries that are online for Sequoyah Co, but he wasn't listed. However, not all cemeteries are listed and the indexes that I did find aren't complete.
There is a volunteer for Sequoyah Co. You'll find his/her contact info at www.gengathering.com. You do need to create a user ID and password to access this web site but access to the volunteer info IS free.
You can attempt to order a copy of his death certificate
from Oklahoma Dept Health, www.ok.gov/health/Birth_and_Death_Certificates/ based on the death info above. Successful Searching!