One week after Steve Jobs announced plans to go on his first medical leave of absence from Apple in 2009, the man tasked with temporarily leading the company — or so it was assumed at the time — had to answer to Wall Street.

Tim Cook joined two other Apple executives for Apple's quarterly earnings call. The first question asked by an analyst on the call was, perhaps unsurprisingly, about Jobs' health and the likelihood that Cook "would be the candidate" to take over as CEO if Jobs were unable to return. Another executive on the call offered a quick boilerplate response to the question. But then Cook chimed in.

"There is extraordinary breadth and depth and tenure among the Apple executive team... And the values of our company are extremely well entrenched," Cook said at the beginning of his response. He then proceeded to lay out those values in a brief monologue that some later dubbed The Cook Doctrine.

We are constantly focusing on innovating. We believe in the simple not the complex. We believe that we need to own and control the primary technologies behind the products that we make, and participate only in markets where we can make a significant contribution. We believe in saying no to thousands of projects, so that we can really focus on the few that are truly important and meaningful to us. We believe in deep collaboration and cross-pollination of our groups, which allow us to innovate in a way that others cannot. And frankly, we don't settle for anything less than excellence in every group in the company, and we have the self-honesty to admit when we're wrong and the courage to change. And I think regardless of who is in what job those values are so embedded in this company that Apple will do extremely well.

That response proved to be an introduction of sorts to investors. Cook had joined Apple in 1998 and emerged as a key executive in charge of the company's increasingly complicated global operations, but he remained relatively unknown. After the earnings call, however, analysts and journalists began praising Cook for having a clear understanding of Apple's DNA and how to run the company with or without Jobs.

In the three years since Cook took over as permanent CEO, a different kind of doctrine has emerged through his rare but growing number of public statements as well as his actions at the company. If his response in 2009 laid out his understanding of Apple's DNA as it was, what we've seen since is a doctrine of how Cook is working to tweak that DNA for the better.

The power of collaboration

When Apple announced the big executive shakeup in 2012 that pushed out then-iOS chief Scott Forstall, the company framed the move in a statement as an effort to "encourage even more collaboration between the company’s world-class hardware, software and services teams."

The statement may have been PR spin on a messy situation, but the choice of the word "collaboration" was more meaningful than that. It's one that Cook has reiterated multiple times in the time since, and it represents a key part of his philosophy for running Apple.

“The lines between hardware, software, and services are blurred or are disappearing,” Cook said in an interview with BusinessWeek published on Wednesday. “The only way you can pull this off is when everyone is working together well. And not just working together well but almost blending together so that you can’t tell where people are working anymore, because they are so focused on a great experience that they are not taking functional views of things.”

Inclusion inspires innovation

In his office at Apple, Tim Cook has pictures of Robert F. Kennedy and Martin Luther King. The pictures, as he explained in a recent interview with Charlie Rose, tie into deeply held notions he has of civil rights.

When asked to describe his most important values personally, he listed off the following: "Treating people with dignity. Treating people the same. That everyone deserves a basic level of human rights regardless of their color, regardless of their religion, regardless of their sexual orientation, regardless of their gender. That everyone deserves respect. I'll fight for it until my toes point up."

While he framed those points as his personal philosophy, it also extends to the company. As he put it in the interview, "Inclusion inspires innovation." He said the same three words in June after marching with thousands of Apple employees in a gay pride parade.

Congrats to 5000 Apple employees/families who attended today’s Pride parade.Inclusion inspires innovation.#applepride pic.twitter.com/4DncX8F6fO — Tim Cook (@tim_cook) June 29, 2014





Improve the world, not just the margins

"We want to leave the world better than we found it," Cook said in the interview with Rose. It's a sentiment Cook has expressed several times and one that explains his visible excitement for Apple's attempts to improve education with the iPad and improve healthcare with the new Apple Watch.

Under Cook's leadership, Apple has started matching employee's charity contributions; it has pushed for 100% renewable energy at some its data centers and its new headquarters; and it has worked to improve conditions in its supply chain (though it may still have a way to go on that last one).

That philosophy of improving the world rather than the company's margins was also in full view earlier this year during Apple's annual shareholder meeting when one person in attendance urged Cook and Apple's board of directors not to pursue environmental initiatives that don't contribute to the company's bottom line.

"We do things because they are right and just and that is who we are. That’s who we are as a company," Cook reportedly said at the meeting. "I don’t…when I think about human rights, I don’t think about an ROI. When I think about making our products accessible for the people that can’t see or to help a kid with autism, I don’t think about a bloody ROI, and by the same token, I don’t think about helping our environment from an ROI point of view."

Pay attention to Wall Street

While the "bloody ROI" may not be his top priority, Cook has repeatedly displayed more of a concern for Wall Street than his predecessor. He has taken more time to meet with investors, presided over massive stock buybacks and even tied some of his bonus to Apple's stock performance.

In the interview with Rose, Cook stressed that employees at Apple are motivated to do good work to help the world rather than the company's market cap. But he was quick to couch that statement. "To all the shareholders out there: I’m not saying I’m not focusing on you," he said. "I’m very focused on them."

Be more transparent about corporate issues, more secretive about products

"Apple" and "transparency" weren't traditionally words people put next to one another, but Cook has made it a point to change that — at least when it comes to issues involving the company's supply chain, environmental efforts and other corporate affairs.

"We decided being more transparent about some things is great — not that we were not transparent at all before, but we’ve stepped it up in places where we think we can make a bigger difference, where we want people to copy us," Cook told Bloomberg BusinessWeek in an earlier interview in 2012.

That said, Cook has decided to continue his predecessor's emphasis on keeping the company's product plans secret, noting in another interview that Apple would "double down on product secrecy."

Don't try to be Steve Jobs

"I’ve never had the objective of being like him," Cook said at one point in the interview with Rose, alluding to Jobs. "The only person I can be is the person I am, right? ... So that’s what I’ve done. I’ve tried to be the best Tim Cook I can be."