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During the course of their relationship, Francina Fernandez and her boyfriend had three boys, who are now adults. The couple never married and in June of 2001 the relationship ended. The two became embroiled in a very lengthy and aggressive custody-visitation dispute in the San Diego Family Court. In early November of 2004, the mother reportedly mentioned to the father that she and the children were planning a 2-week vacation in New Zealand. He told her that the trip would violate the court orders, and Fernandez's attorney was served with a notice of an ex-parte hearing scheduled for November 8, 2004.  At the hearing, a judge ordered that neither parent could take the children out of the jurisdiction of the court and that the children's passports were to be relinquished. The passports were never returned. Also, in November it was reported that Fernandez abruptly left her job and a relative filed a missing person's report for her. Fernandez may have fled with her children to the Philippines.

On December 9, 2004, a state warrant was issued in the state of California, San Diego County, charging Francina Dacanay Fernandez with three counts of child abduction. A federal arrest warrant was subsequently issued on February 4, 2005, in the United States District Court, Southern District of California, charging Fernandez with international parental kidnapping.