The first participants in the sanctuary movement initially called it a "civil initiative." The movement drew on statements that the United States had made in the Nuremberg trials. It had argued that there exists a standard higher than that set by government, one to which all people should adhere even when ordered to do otherwise. Similarly, the organizers believed that they too had a duty to help refugees whose lives were threatened in their native countries, to help them escape danger and enter the US even if they were not legally allowed to do so. The US government, however, refused to acknowledge this reasoning, claiming Central American refugees were simply economic migrants.
After three years of publicly helping refugees across the border, the sanctuary movement was unlawfully infiltrated by the FBI. Its phones were tapped, and an agent was found to be working within the group. As a result, many participants were indicted and tried.

Reverend John Fife spent six months in jail awaiting his trial. Once the trial began, the judge, when setting the rules for the court, prohibited all mention of refugees, human rights abuses, Central American wars, and many other pertinent issues. This deprived Reverend Fife and his supporters of the ability to explain their cause and their justification for breaking immigration law. They appealed, filing a suit against the attorney general, and the government eventually decided to negotiate a settlement instead of continuing the trial.

In 1989, the government finally agreed to grant temporary protected status and work permits to those refugees who were already in the US. Those who registered between 1989 and 1992 also received protection. However, there exists no such provision for Central American refugees who have entered since 1992.

Tucson's Southside Presbyterian Church was the first location to declare sanctuary for Central American refugees in the early 1980's. As civil wars were going on in many Central American nations, a steady stream of people fled the terror of death squads and armies. Mexico first opened its borders to these refugees, many of whom were willing to leave behind their homes and families to escape torture, rape and death, and many of whom were not fortunate enough to have escaped those things. However, Mexico then closed its borders during the devastating depression of 1981 in order to recover internal economic stability. The US government supported Mexico in this effort.

Consequently, it became infinitely harder for refugees to arrive at the US because they now had to face Mexican officials in addition to the U.S. Border Patrol. Women suffered most; often the only way in which they were allowed passage was through sex, and by the time they came into the US they had been raped a great number of times. The refugee's road to peace, although justified by the UN Declaration of Human Rights, had become extremely difficult.

It is in response to these growing obstacles that the sanctuary movement arose. During its activity, the movement's volunteers investigated the veracity of those who claimed to be refugees through a network of churches and human rights groups that spread through Central America. They then physically helped the refugees across the American border and housed them in any available accommodations. The Tucson church alone welcomed more than 12,000 refugees over the course of the movement. Eventually, the refugees were established in different locations around the US and sometimes even Canada through an underground railroad that had developed for the purpose.

The movement itself was not hierarchically structured, consisting of an organizing group and an obedient body of members. Instead, it connected faith-based communities, human rights groups, and secular organizations such as the UCs and the State of New Mexico, along the border and across the nation. Stanford University also participated, housing a Central American refugee in the Columbae House. Such a structure lacked a conspicuous head of command and thus protected the movement from easy destruction. Even while certain groups were forced to discontinue their activity, others were able to go on.

The movement was very successful and gained international acknowledgment. In many ways, it still continues. Southside Church, for example, now houses the Center for Prevention and Resolution of Violence, treatment program for refugee torture victims, lavishing great care and support to people from all over the world. Led by Father Ricardo Elford and Amy Shubitz, the center not only provides medical and psychological services, but helps people get acquainted with Tucson life, assists families with school and higher education, and gladly hosts all sorts of community and family events. Its members treat everyone with personal attention and unwavering warmth, and still keep in touch with the refugees whom they had hosted during the movement.