Police have since arrested all of the suspects, and the school lockdowns were lifted at 12:42 p.m., Fremont police Detective Bill Veteran said.
The search started at around 11:30 a.m. when a homeowner in the 4300 block of Stanley Avenue told police he had arrived home to find three people inside his residence, Veteran said.
As the intruders escaped, there was a brief scuffle with the homeowner, who suffered minor injuries, Veteran said.
Veteran also said that the homeowner saw at least one of the intruders with a gun, but it was unclear whether the suspect had threatened the homeowner with it.
Police arrived at the scene shortly after that and locked down Irvington High School at 41800 Blacow Road at 11:55 a.m. as a precaution, Fremont Unified School District employee Sharon Coco said.
As the search expanded, police locked down Steven Millard Elementary School at 5200 Valpey Park Ave. at 12:15 p.m. and Robertson High School at 4455 Seneca Park Ave. at 12:30 p.m., Coco said.
Veteran said the three suspects were caught at different locations.
"They got about a half-mile from there -- they made good time -- but we caught them with the help of the East Bay Regional Parks helicopter," Veteran said.
Veteran said the three suspects are all male, and at least one is an adult. He did not yet have more information on the suspects.