From 2002, William (Bill) Buckingham and Alan Bonsell, members of the Dover Area School District Board of Education who were young earth creationists, had made various statements supporting teaching creationism alongside evolution. At a board meeting on June 7, 2004, Buckingham mentioned creationism and raised objections to the proposed use of the textbook Biology written by Kenneth R. Miller and Joseph S. Levine, describing it as "laced with Darwinism" and saying it was "inexcusable to have a book that says man descended from apes with nothing to counterbalance it."
This story made the York newspapers, and Buckingham was telephoned by Discovery Institute staff attorney Seth Cooper, whose tasks included "communicating with legislators, school board members, teachers, parents and students" to "address the topic of ID in a scientifically and educationally responsible way" in public schools. He later stated that he made the call to "steer the Dover Board away from trying to include intelligent design in the classroom or from trying to insert creationism into its cirriculum", an account Buckingham has disputed. Cooper sent the book and DVD of Icons of Evolution to Buckingham, who required the Dover High School science teachers to watch the DVD. They did not take up the opportunity to use it in their classes.
Cooper advised that the Discovery Institute was not offering legal advice, and soon afterwards Buckingham contacted Richard Thompson of the Thomas More Law Center, who agreed to represent the Dover Board, and recommended the book Of Pandas and People. On October 18, 2004, the school board voted 6-3 resolving that there were to be lectures on the subject, with Pandas as a reference book, and that the following statement was to be added to their biology curriculum: "Students will be made aware of the gaps/problems in Darwin's theory and of other theories of evolution including, but not limited to, intelligent design. Note: Origins of life is not taught."
On November 19, 2004, the Dover Area School District issued a press release stating that, commencing in January 2005, teachers would be required to read the following statement to students in the ninth-grade biology class at Dover High School:
The Pennsylvania Academic Standards require students to learn about Darwin's theory of evolution and eventually to take a standardized test of which evolution is a part.
Because Darwin's Theory is a theory, it is still being tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.
Intelligent design is an explanation of the origin of life that differs from Darwin's view. The reference book Of Pandas and People, is available for students to see if they would like to explore this view in an effort to gain an understanding of what intelligent design actually involves.
As is true with any theory, students are encouraged to keep an open mind. The school leaves the discussion of the origins of life to individual students and their families. As a standards-driven district, class instruction focuses upon preparing students to achieve proficiency on standards-based assessments.
-- (page 1 of decision)
The three school board members who voted against it resigned in protest, and science teachers in the district refused to read the statement to their ninth-grade students, citing the Pennsylvania state code 235.10(2), which requires that "The professional educator may not ... Knowingly and intentionally misrepresent subject matter or curriculum." Instead, the statement was read to students by a school administrator.
The school board's statement asserting that there are "gaps" in evolution and that it specifically is a theory "not a fact" singled out evolution, implying it is just a hunch, even though this is not the actual meaning of the term "scientific theory". The reference to Of Pandas and People and presentation of intelligent design as an alternative "explanation of the origins of life" presented it as though it were a scientific explanation, in contrast to the way that evolution was described. Encouraging students to "keep an open mind" about alternatives without offering an alternative scientific explanation implied an invitation to meditate on a religious view, endorsing the religious view in a way similar to the disclaimer found to be unconstitutional in the Freiler v. Tangipahoa Parish Board of Education case. The school board claimed the statement does not teach intelligent design and simply makes students aware of its existence as an alternative to evolution, but no such statements were made about other subjects. As part of the presentation, the administrators stated that "there will be no other discussion of the issue and your teachers will not answer questions on the issue", giving intelligent design a position not applied to scientific topics. The board denied that intelligent design was "religion in disguise," despite being represented in court by the Thomas More Law Center, a conservative Christian not-for-profit law center that uses litigation to promote "the religious freedom of Christians and time-honored family values". Its stated purpose is "... to be the sword and shield for people of faith".
The American Civil Liberties Union filed suit on December 14, 2004, on behalf of eleven parents from the Dover school district, and sought a law firm willing to take on the case at the risk of not being paid if the case was lost. Eric Rothschild, a partner at Pepper Hamilton LLP and a member of the National Center for Science Education legal advisory council, was quick to agree to take the case on such a contingency basis.
The Discovery Institute's John West said the case displayed the ACLU's "Orwellian" effort to stifle scientific discourse and objected to the issue being decided in court. "It's a disturbing prospect that the outcome of this lawsuit could be that the court will try to tell scientists what is legitimate scientific inquiry and what is not," West said. "That is a flagrant assault on free speech." Opponents, represented by the American Association for the Advancement of Science and the National Association of Biology Teachers, contended that his statement is not just ironic, but hypocritical, as the Discovery Institute opposes methodological naturalism, the basic principle that limits science to natural phenomena and natural causes without assuming the existence or non-existence of the supernatural, which by definition is beyond natural explanation.
Despite its earlier involvement, the Discovery Institute was concerned that this would be a test case and that the defendants had earlier displayed their religious motivations. This tension led to disagreements with the Thomas More Law Center and the withdrawal of three Discovery Institute fellows as defense experts prior to their depositions - William A. Dembski, Stephen C. Meyer and John Angus Campbell. This was purportedly because the Thomas More Law Center refused to allow these witnesses to have their own attorneys present during deposition, but Discovery Institute director Bruce Chapman later said that he had asked them not to testify (as well as Behe and Minnich, who testified anyway).
In May 2005, the publisher of Of Pandas and People, the Foundation for Thought and Ethics (FTE), filed a motion seeking to intervene in the case. FTE argued that a ruling that intelligent design was religious would have severe financial consequences, citing possible losses of approximately half a million dollars. By intervening, FTE would have become a co-defendant with the Dover Area School Board, and able to bring its own lawyers and expert witnesses to the case. FTE's president Jon Buell implied that if allowed to intervene, FTE would bring Dembski and Meyer as expert witnesses. In his decision on the motion, Jones ruled that FTE was not entitled to intervene in the case because its motion to intervene was not timely, describing FTE's reasons for not trying to become involved earlier as "both unavailing and disingenuous." Jones also held that FTE had failed to demonstrate that it has "a significantly protectable interest in the litigation warranting intervention as a party" and that its interests would not be adequately represented by the defendants.
In the November 2005 elections, none of the members of the Dover School Board who voted for the intelligent design policy were re-elected, and a new school board, which rejected the policy, took office. This effectively precluded the possibility of an appeal to a higher court.