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Day after day, night after night, Francisco Hernandez Jr., 13 years old, rode the subway. He had an electronic fare card, $10 in his pocket and a bookbag on his lap. As the human tide flowed and ebbed around him, he sat impassively, a gangly boy in glasses and a red hoodie, speaking to no one.

After getting in trouble in class in Bensonhurst, Brooklyn, and fearing another scolding at home, he had sought refuge in the subway system. He removed the battery from his cell phone. “I didn’t want anyone to scream at me,” he said.

Francisco disappeared for 11 days in October — a stretch he spent entirely in subway stations and on trains, he says, hurtling through four boroughs. And somehow he went undetected, despite a round-the-clock search by his panicked parents, relatives and family friends, the police and the Mexican Consulate.

Since Oct. 26, when a transit police officer found him in a Coney Island subway station, no one has been able to fully explain how a boy could vanish for so long in a busy train system dotted with surveillance cameras and fliers bearing his photograph.

But this was not a typical missing-person search. Francisco has Asperger’s syndrome, a form of autism that often causes difficulty with social interaction, and can lead to seemingly eccentric behavior and isolation. His parents are Mexican immigrants, who say they felt the police were slow to make the case a priority.

“Maybe because you might not understand how to manage the situation, because you don’t speak English very well, because of your legal status, they don’t pay you a lot of attention,” said Francisco’s mother, Marisela Garcia, 38, a housecleaner who immigrated in 1994 and has struggled to find ways to help her son.

The police, however, say they took the case seriously from the start, interviewing school officials and classmates, canvassing neighborhoods and leafleting all over the city.

Francisco says his odyssey wound through three subway lines: the D, F and No. 1. He would ride a train until its last stop, then wait for the next one, wherever it was headed. He says he subsisted on the little he could afford at subway newsstands: potato chips, croissants, jelly rolls, neatly folding the wrappers and saving them in the backpack. He drank bottled water. He used the bathroom in the Stillwell Avenue station in Coney Island.

Otherwise, he says, he slipped into a kind of stupor, sleeping much of the time, his head on his bookbag. “At some point, I just stopped feeling anything,” he recalled.

Though the boy’s recollections are incomplete, and neither the police nor his family can retrace his movements in detail, the authorities say that he was missing for 11 days and that they have no evidence he was anywhere but the subway.

For his parents, the memories of those 11 frantic days — the dubious sightings, the dashed hopes and no sleep — remain vivid.

What propelled Francisco to take flight on Oct. 15 is unclear.

Administrators at his school, Intermediate School 281, would not comment. But Francisco said he had failed to complete an assignment for an eighth-grade class, and was scolded for not concentrating.