Search warrants, raids, arrests, and now court appearances. The terrorism investigation took a major step Monday. Only something is missing: actual terrorism charges.

Three Afghan men living in the United States have been arrested - including Najeebulah Zazi, his father in Denver and Ahmad Wais Afzali, an imam at a mosque in Flushing, Queens. All three are accused of lying to the FBI about their connection to an alleged New York terror plot.

Zazi - who allegedly received al-Qaida training on explosives - is the central focus of the terrorism investigation. The FBI said it found 9 pages of bomb making notes on his computer and sources say last week yielded more than a dozen backpacks from his apartment.

With subway bombings, like those in Madrid and London in mind, the FBI and homeland security Monday reissued a warning for rail and transit systems. In total, New York City subways and buses carry 8 million people a day. More random sweeps and patrols in the city are likely.

The New York connection, Afzali, is a 37-year-old funeral home worker, who worked out a deal to stay in New York by becoming an informant. The FBI went to Afzali last week for information on Zazi. But officials say Afzali instead tipped off the 24-year-old Denver man.

Afzali's lawyer, Ron Kuby, says his client is being made a scapegoat for a botched investigation.