The civil rights suit, filed in federal court Tuesday, names the Heritage Foundation, a conservative think tank, as the architect of what it describes as an ongoing conspiracy to silence members of the pro-Palestinian movement by smearing them as antisemites.
Those efforts were aided by Canary Mission and Betar, two pro-Israel groups that maintain online lists of Israel's critics, often alongside unsubstantiated claims that they are affiliated with Hamas, according to the lawsuit.
Activists placed on those lists "were nearly automatically targeted by the Federal Defendants for arrest and removal," the suit claims, adding that the "process of nomination to punishment was frictionless."
Lawyers for Khalil argue this "public-private partnership" could violate the Ku Klux Klan Act, a Reconstruction-era law that sought to restrict government coordination with vigilante groups. Their suit seeks unspecified damages and a judicial order to end the conspiracy.
Inquiries to the Heritage Foundation, Canary Mission and Betar were not immediately returned on Tuesday.
Abigail Jackson, a White House spokesperson, did not comment on the lawsuit, but said in an email that the executive branch "has the lawful authority to take actions that will protect the public and to ensure the integrity of our immigration system."
The suit comes as Khalil's deportation case appears headed to the U.S. Supreme Court.
At a news conference on Tuesday, Khalil described the purpose of the latest filing as "exposing the network of organizations, particular actors and institutions that work together to criminalize solidarity with Palestine and to make an example of those who refuse to stay silent."
"If constitutional protections can be cast aside under political pressure today, they can be cast aside tomorrow against anyone," he added.
A former graduate student at Columbia University, Khalil gained prominence as a spokesperson and leader for student activists protesting against Israel and its actions in Gaza.
He was arrested in March 2025 by U.S. Immigration and Customs Enforcement agents in his campus apartment and quickly became the face of the Trump administration crackdown on pro-Palestinian demonstrators.
Khalil then spent 104 days in a Louisiana immigration jail, missing the birth of his first child, before a federal judge in New Jersey ordered his release.
Soon after his arrest, both Canary Mission and Betar boasted of their role in flagging Khalil's noncitizen status to the government.
Betar - an Israeli company that claimed to use facial recognition software to identify masked protesters - also claimed it had compiled a longer list of names and given it to the Trump administration. The group has since agreed to dissolve its nonprofit status, following a lawsuit filed by New York Attorney General Letitia James accusing its members of harassing Palestinians.
Khalil's lawsuit traces the origins of the alleged conspiracy to a blueprint from the Heritage Foundation, entitled "Project Esther," which called for the expulsion of noncitizens who joined protests against Israel.
The report also suggested, without evidence, that participants in those protests should be seen as part of a "highly organized, global Hamas Support Network."
In May, as the Trump administration ramped up its crackdown on pro-Palestinian activists, one of the report's authors, Robert Greenway, appeared to acknowledge the foundation's influence, saying that it was "no coincidence that we called for a series of actions to take place privately and publicly, and they are now happening," according to the suit.
Greenway, a former adviser to Trump, did not reply to a request for comment.
Khalil, meanwhile, has forcefully denied that his criticism of Israel amounts to antisemitism. While government officials - along with Canary Mission and Betar - have linked him to Hamas, they have offered no evidence to support the claim.
"My beliefs are not wanting my tax money or tuition going toward investments in weapons manufacturers for a genocide," Khalil previously told The Associated Press. "It's as simple as that."