It all stems back to the death of San Francisco Public Defender Jeff Adachi on February 22.
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A day after that, freelance journalist Bryan Carmody obtained the police report on Adachi's death and sold it to ABC7 and other stations.
RELATED: San Francisco mayor orders independent investigation into raid on journalist's home
In April, police asked Carmody to reveal his source for the report, but he refused.
On May 10, police then raided Carmody's home, seizing thousands of dollars of equipment.
RELATED: I-Team questions police chief about raid on journalist's home, Jeff Adachi investigation
Press groups across the country protested the raid.
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Earlier this week a judge ordered the police to return Carmody's equipment. And Scott said Carmody is under investigation for "criminal conspiracy."
And now the I-Team's Dan Noyes pressed the chief to apologize to Carmody after the graduation of the 263rd police academy at the Scottish Rite Masonic Center.
Scott: "We do, I owe an apology."
Noyes: "To whom?"
Scott: "To the people of San Francisco."
Noyes: "How about to Bryan Carmody?"
Scott: "To Bryan Carmody, as well."
Noyes: "Why?"
Scott: "We made some mistakes."
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Get the latest details on this developing story here.
Take a look at for a look at more stories by Dan Noyes and the ABC7 News I-Team.