The major controversy was over her effort to build a Planned Parenthood clinic on the reservation after the South Dakota legislature banned most abortions throughout the state.
In 1963 her family moved from the reservation to Los Angeles, California, in a Bureau of Indian Affairs-sponsored urban relocation program.
[3] In 1986, Cecilia returned to the Pine Ridge Reservation, where she was given the Lakota name of Good Hearted Woman for her services and advocacy for Native American healthcare.
[2] After more than 20 years away, in 1986 Fire Thunder returned to the Pine Ridge Reservation and started work at the Bennett County Hospital.
[5] In her work for Cangleska, Inc., a domestic violence shelter, she also dealt with women who suffered from abuse related to poverty and alcoholism on the reservation.
On November 2, 2004, Cecilia Fire Thunder was elected as the first female president of the Oglala Sioux Tribe of the Pine Ridge Reservation to serve the two-year term.
She defeated both Russell Means, notable as an activist in the American Indian Movement (AIM), and the incumbent John Yellow Bird Steele.
Fire Thunder said the allegations were false, and she had openly negotiated the loan as part of straightening out the tribe's financial status.
In a unique agreement, the state proposed to deputize OST police (additional staff to be hired) to patrol Whiteclay to prevent beer from being transported to the reservation.
She believed that her constituents needed full family planning services, and that the sovereign reservation would not be subject to state laws.
In 2004 public opinion polls had shown that 68% of people surveyed in South Dakota supported options for abortions in some cases, so the new law generated controversy across the state.
Other charges were that Fire Thunder used the media, the U.S. Post Office and the Oglala Sioux Tribe to solicit funds for the clinic.
On June 30, 2006, Alex White Plume, tribal vice-president, assumed the role of President Pro Tem, which he held until the November 2006 election.
[11] The council and succeeding chief never organized to spend the federal grant money to support deputized police to patrol at Whiteclay, and the funds were rescinded in late 2007.
[12] During the same period, in 2006 and 2007 tribal activists held blockades on the road inside the reservation to prevent beer from being brought from Whiteclay and continued to demand action by Nebraska.
During the trial she was told that she had six charges against her, but the councilmen only voted on one charge and that was what they all talked about during the trial; “[She] invited federal and state law onto our sovereign reservation by challenging the new state abortion law, to begin her own abortion clinic, under the auspices of the Oglala Sioux Tribe.” The letter of suspension that was written educated her about how she could not "... she would not conduct any business in the name of the OST, was banned from discussing her case with media (on or off the reservation), that no further contributions would be accepted, that any monies received for the clinic would be returned, and that she could not travel on behalf of the tribe".