Isabella's parents, Janet Jenkins and Lisa Ann Miller, were lesbian partners. They met in 1997 and moved in with each other a few weeks later. In December 2000, the couple were joined in a civil union in Vermont. (Their home state of Virginia does not recognize civil unions.) In 2001, they made the decision to become parents and Lisa conceived Isabella with sperm from an anonymous donor. Janet never legally adopted her. Four months after the child's birth, the family moved to Fair Haven, Vermont. Lisa had fertility treatments to try to have another baby, but wasn't able to. The couple lived as Unitarians.

In 2003, Lisa and Janet ended their relationship amicably and Lisa moved back to Virginia with Isabella. The women had an informal agreement where Janet would pay child support and have regular visits with Isabella, but their cooperation ended in 2003, after Lisa joined the Thomas Road Baptist Church, a conservative congregation founded by evangelist Jerry Falwell (founder of Liberty University), and renounced her homosexuality. She now believes homosexuality is a sin.

When Judge William Cohen in Vermont dissolved the couple's civil union in 2004, he gave custody of Isabella to Lisa and liberal visitation to Janet. Lisa regularly refused to allow Janet access to Isabella, however, because she felt Janet was not the child's mother but rather a "friend." She testified that Janet was a physically and emotionally abusive partner, and she also accused Janet of sexually abusing Isabella. Janet denied these allegations under oath, and Virginia's Child Protective Services deemed the abuse accusations unfounded. Judge Cohen fined Lisa $25 for every day she refused to let Janet see Isabella, and he made the ruling retroactive. Lisa quickly accumulated thousands of dollars in fines.

Lisa fought the case up to the state supreme court of both Vermont, which decided against her, ruling that Janet was Isabella's legal parent and the case was the same as any custody dispute between heterosexual parents. Lisa then tried to change jurisdiction to Virginia. The lower courts sided with her, but the Virginia Court of Appeals ruled that Vermont had jurisdiction. The United States Supreme Court declined to hear the case. On November 20, 2009, Judge Cohen found Lisa in contempt of court and awarded custody of Isabella to Janet, saying this was the only way the child would be able to spend time with both parents.

Lisa took Isabella and disappeared sometime in the fall of 2009. It's unclear exactly when, but her neighbors said they hadn't seen her since September. Investigators believe she initially took Isabella to Canada and then to Mexico. She was supposed to turn the child over to Janet on January 1, 2010, but she never did. Judge Cohen gave her 30 days to comply with the ruling, then found her in contempt of court and issued a felony warrant for her arrest on charges of kidnapping.

In April 2011, Timothy David "Timo" Miller (no apparent relation to Lisa) was arrested in Alexandria, Virginia and charged with aiding and abetting Lisa and Isabella's flight. He is a Mennonite missionary in Nicaragua and authorities believe he helped Lisa and Isabella leave the United States and move to a "safe house" in the capital city of Managua. In October, authorities dropped the charges against Timothy in exchange for his cooperation in the investigation.

Kenneth L. Miller (no relation to Lisa or Timothy) was indicted for aiding international parental kidnapping in December 2011. A pastor with the Beachy Amish-Mennonite Church in Stuart's Draft, Virginia, he allegedly aided Lisa and Isabella's flight by having fellow Amish-Mennonites purchase plane tickets for them to fly to Canada and then on to Nicaragua. The two females were wearing the long dresses Mennonite women wear; Kenneth had purchased them. In Nicaragua, they initially stayed with Amish-Mennonite missionaries on a rural farm. Lisa homeschooled Isabella, who used the name "Lydia" and learned to speak Spanish. Kenneth was convicted in March 2013 and sentenced to 27 months in prison, but he won't have to start serving his sentence until the outcome of his appeal is decided. Citing religious reasons, he has refused to testify against others whom authorities believed have helped hide Isabella and Lisa.

In August 2012, Jenkins filed a filed a civil Racketeer Influenced and Corrupt Organizations (RICO) suit against Lisa, Kenneth, Timothy, the Liberty University School of Law, the Thomas Road Baptist Church and others, alleging they'd all assisted in Isabella's abduction and conspired to keep the child hidden. The suit is pending.

The Miller-Jenkins custody battle has made national headlines because of the issues it involves. Isabella and Lisa may still be in Nicaragua, or they may be in El Salvador. Authorities continue to search for Isabella. Her case remains unsolved.