Passengers were buckled up and waiting to depart in London when the crew told them they couldn't take off with the mouse on board.
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One passenger tweeted "Just had my flight to SFO canceled because of a mouse on board the plane. Could it not get a Visa?"
The crew joked that the mouse couldn't enter US airspace without a passport, and told everyone they needed a whole new plane. That meant a four-hour delay.
They told KGO-TV in San Francisco after the flight arrived Wednesday that despite the delay most passengers were happy to be on a mouse-free aircraft, especially knowing they'd be eating on the flight.
British Airways apologized and said they were satisfied that only passengers with two legs were on the flight.
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The flight arrived in San Francisco Wednesday evening.
The Associated Press contributed to this report.