Brown, who joined Google from McKinsey in 2003, has remained as under the radar as Mayer floated above it. Highly analytical and introverted, Brown has spent the bulk of her Google career overseeing Business Operations—advising senior management on business strategy, organizational structure and bureaucracy-busting efforts as the company expanded from 1,000 to over 30,000 employees during her tenure.

A Rhodes scholar with a PhD in engineering, Brown, 46, fit into Google’s brainiac culture but long ago left the fast track to a top role in the company. Five years ago, while in charge of Business Operations, she gave up oversight of People Operations—HR-plus—to Laszlo Bock, another SVP. Brown meanwhile reduced her work schedule to 70% of normal Google hours, aiming to have time for outside board work.

In fact, many Google watchers say that Brown “retired” years ago. But she got one thing that she wanted: a plum board seat at PepsiCo in 2009. As Brown has helped Pepsi CEO Indra Nooyi navigate her global growth challenges, her influence inside Google has further waned. When co-founder Larry Page succeeded Eric Schmidt as chief executive early last year, Brown (like Mayer) lost her place in the CEO’s inner circle and got sidelined. Page asked Brown to head Google.org, the company’s philanthropy arm. She was game. “I felt I had made my mark,” Brown says, “and I was beginning to feel the itch about social impact.”

So for the past two years, Brown has been working on this question: How best to use technology to tackle social problems around the world? She has focused Google.org on three areas: expanding Internet access, developing cleaner energy, and strengthening citizen engagement. On the latter challenge, Google.org provided the first live election results map in Mexico’s history.

Friday morning at Google headquarters in Mountain View, California, Brown convened her Google.org team and told them that she’s ready to go. Unlike Mayer, she doesn’t have a high-profile CEO job lined up. She’s simply planning to set up shop to advise “social entrepreneurs and regular entrepreneurs on all the challenges of growth,” she says.

“It’ll be fun to take the lessons I learned at Google,” Brown adds. And what might they be? She ticks off three:

1. “People are the most important thing.”
2. “Integrity is as important as brilliance.”
3. “You don’t have to have the highest IQ or EQ–but some combination–to add value to geeks and brainiacs.”

While Google has come under scrutiny lately for its dearth of senior woman, the most influential female executive shows no sign of going anywhere. Susan Wojcicki has been at Google ever since she rented her Silicon Valley garage to two guys named Larry Page and Sergey Brin when they were dreaming up a company to organize the web. A key builder of Google’s ad platforms and now SVP of Product Management and Engineering, Wojcicki ranks No.18 on Fortune’s Most Powerful Women list.

Asked if Google has a problem retaining senior women, Brown replies, “The sector has a problem.” Google, she says, has made huge efforts to find and recruit female tech talent, particularly computer scientists.

After having two women bosses—Brown and Megan Smith before her—Google.org now gets a guy in charge: Mathew Stepka, who has been VP of Business Operations at Google for five years. “The organization will survive and thrive,” vows Brown, who has another important item on her post-Google agenda. She’s engaged to be married.