Jones' interests also extend to archaeometry, solar energy, and, like many professors at BYU, archaeology and the Book of Mormon. For example, he has sought radiocarbon dating evidence of the existence of pre-Columbian horses in the Americas, and has interpreted archaeological evidence from the ancient Mayans as supporting his faith's belief that Jesus Christ visited America.
Around 1985 Jones then became interested in the anomalous concentration of helium-3 found in the gases escaping from volcanoes. He hypothesized that the high pressures in the Earth's interior might make fusion more likely, and began a series of experiments on what he referred to as piezofusion, or high-pressure fusion. In order to characterize the reactions, Jones designed and built a neutron counter able to accurately measure the tiny numbers of neutrons being produced in his experiments. The counter suggested a small amount of fusion was going on. Jones said the result suggested at least the possibility of fusion, though the process was unlikely to be useful as an energy source.
Pons and Fleischmann (P&F) started their work around the same time. Their work was brought to Jones' attention when they applied for research funding from the Department of Energy, after which the DOE passed their proposal along to Jones for peer review. Realizing their work was very similar, Jones and P&F agreed to release their papers to Nature on the same day, March 24, 1989. However, P&F announced their results at a press event the day before. Jones faxed his paper to Nature.
A New York Times article says that while peer reviewers were quite critical of Pons and Fleishchmann's research they did not apply such criticism to Jones' much more modest, theoretically supported findings. Although critics insisted that his results likely stemmed from experimental error, most of the reviewing physicists indicated that he was a careful scientist. Later research and experiments supported the metallic cold fusion reports by Jones.
He subsequently defended the research twice more at BYU, also at Idaho State University, Utah Valley State College, University of Colorado at Boulder and University of Denver, the Utah Academy of Science, Sonoma State University, University of California at Berkeley, and the University of Texas at Austin.
Jones' paper has been the center of controversy both for its content and its claims to scientific rigor. Jones' early critics included members of BYU's engineering faculty; shortly after he made his views public, the BYU College of Physical and Mathematical Sciences and the faculty of structural engineering issued statements in which they distanced themselves from Jones' work. They noted that Jones' "hypotheses and interpretations of evidence were being questioned by scholars and practitioners," and expressed doubts about whether they had been "submitted to relevant scientific venues that would ensure rigorous technical peer review.
Some of Jones' colleagues have defended his work on 9/11 to varying degrees, and Project Censored lists his 9/11 research among the top mainstream media censored stories of 2007.
Jones maintains that the paper was peer-reviewed prior to publication within a book "9/11 and American Empire: Intellectuals Speak Out" by D.R. Griffin, however it has never been published in an independent peer-reviewed journal. The paper was also posted on the Internet site of the "Journal of 9/11 Studies", which was co-founded by Jones for the purpose of "covering the whole of research related to 9/11/2001", was co-edited by him, and which has recently slowed publication, having posted a notice that potential contributors were encouraged to submit their prospective work to other, more mainstream, publications.The paper also appears in Global Outlook, a magazine "seeking to reveal the truth About 9/11 and in a volume of essays edited by David Ray Griffin and Peter Dale Scott.
The university cited its concern about the "increasingly speculative and accusatory nature" of Jones' work and the concern that perhaps it had "not been published in appropriate scientific venues" as reasons for putting him under review. The review was to have been conducted at three levels: BYU administration, the College of Physical and Mathematical Sciences, and the Physics Department.
Jones' placement on paid leave drew criticism from the American Association of University Professors and the Foundation for Individual Rights in Education. Both organizations are long time critics of BYU's record on academic freedom. Jones "welcomed the review" because he hoped it would "encourage people to read his paper for themselves," however the review was abandoned (contrary to Jones' request) when Jones elected to retire, effective January 1, 2007.
Jones has been interviewed by mainstream news sources and has made a number of public appearances. While Jones has urged caution in drawing conclusions, his public comments have suggested a considerable degree of certainty about both the controlled demolition of the World Trade Center and the culpability of rogue agents working within the U.S. government. In one interview, he asserted that the attacks were "an 'inside job', puppeteered by the neoconservatives in the White House to justify the occupation of oil-rich Arab countries, inflate military spending, and expand Israel. His name is often mentioned in reporting about 9/11 conspiracy theories.
In April 2008, Jones, along with four other authors, published a letter in The Bentham Open Civil Engineering Journal, titled, 'Fourteen Points of Agreement with Official Government Reports on the World Trade Center Destruction'. And in August 2008, Jones, along with Kevin Ryan and James Gourley, published a peer-reviewed article in The Environmentalist, titled, 'Environmental anomalies at the World Trade Center: evidence for energetic materials'..
Jones is a member of The Church of Jesus Christ of Latter-day Saints.
Jones has been described as "a devout Mormon and, until recently, a faithful supporter of George W. Bush." However, Jones himself noted that he did not vote for Bush/Cheney, and he called for their impeachments beginning at large conferences in Chicago and Los Angeles in June 2006.
Jones is co-editor of Journal of 9/11 Studies.