It looks like the Department tried to pull a fast one and was called on it by the Judge. It initially claimed it didn't examine the one drug protocol because the Supreme Court had already determined in Baze v Kentucky that the three drug cocktail was not unconstitutional. It wrote in its initial brief:

As an integral part of the review, the CDCR considered alternatives to the existing three-chemical process, including a one-chemical process. Additionally, in developing this proposed regulation, the CDCR was guided by the United States Supreme Court’s decision in Baze v. Rees (2008)...

The judge said that was "patently false" as the decision to adopt the three-drug protocol was decided in May 2007, before the decision in Baze v. Rees (2008). The Department then conceded it was wrong in using Baze v. Rees as an excuse, and admitted that Governor Schwarzenegger had approved the new three drug protocol in 2007.

It also failed to substantiate that it considered the one-drug method.

There were other deficiencies. There was no inclusion of the cost of the new execution protocols as required by state law.

The judge noted that former San Quentin Prison Warden Jeanne Woodford said each execution costs the state between $70,000 and $200,000 in overtime for staff, crowd control, training, security and other expenses associated with carrying out lethal injections.

The judge also said prison officials failed to reply to the public comments as state law mandates before adopting the new protocols. Nor did they properly notify the condemned 720 inmates of the new procedures.

In addition, the judge questioned the need for some of the protocols, such as requiring unit staff to monitor the inmate every 15 minutes and document their findings for five days before the execution, or to remove all property from the inmate's cell, or to impose waist restraints during visits.

The judge concludes:

These defects infect the entire regulatory scheme, and the lethal injection administration and protocol, as a whole, is declared to be invalid.

The case was assigned to Marin County because San Quentin is located there.

After six years, California's death penalty system remains broken. As for where it goes from here:

Prison officials would either have to appeal or again revise their lethal injection procedures and submit them to public comment, a process that took more than a year last time.

Or, they can just give up and end the death penalty, converting the death sentences to life without parole.