The attacker struck close to midnight, climbing into a manhole at the mouth of California’s Niles Canyon and slicing a series of cables that collectively carried billions of bits of Internet data.

Hundreds of miles away at a Zayo Group Holdings Inc. network operations center in Tulsa, Okla., engineers saw the disruption immediately and later a second break made further up the road the same February night.

As monitoring software lighted up with red bars indicating several circuit failures, technicians pinpointed the breaches at a familiar place—the site of two previous cuts. Several months later, in June, Fremont, Calif., police reported a fifth cut.

The Federal Bureau of Investigation says San Francisco’s Bay Area has suffered more than a dozen attacks on its fiber optic infrastructure over the past year. The attacks slow Internet service and disrupt financial transactions and emergency phone calls.

The way the cuts are clustered on single nights around the East Bay and in San Jose, Calif., at the heart of Silicon Valley, have led officials to believe the attacks are intentional. Beyond that, they have yet to nail down a motive, let alone a culprit, creating an unusual cyber whodunit with few leads and little understanding.