"At a base level, it shows a lack of understanding about how the design team works and how Apple works," Cook wrote in the email. "It distorts relationships, decisions and events to the point that we just don't recognize the company it claims to describe."

But the Journal's report spurred a lot of discussion and confusion about the current state of Apple, and it drew a rare response from Cook by late Monday afternoon.

Usually when a highly critical story about Apple comes out, the company remains silent and lets it blow over. (Apple initially declined to comment on the Journal's story Sunday.)

The Journal's article painted a picture of a checked-out executive who didn't show up to important meetings and spent his last few years at Apple taking a hands-off approach to leading Apple's design team. The story also implied that the company became less focused on the breakthrough products Ive is known for and more focused on its operations and other initiatives under CEO Tim Cook's leadership.

The buzz of the tech world this week was a new report from The Wall Street Journal that charted the last few years of Apple's Chief Design Officer Jony Ive before his announced departure last Thursday .

Apple CEO Tim Cook (L) and Jonathan Ive, Apple's Chief Design Officer, look over the new Mac Pro Display and computer at Apple's Worldwide Developer Conference (WWDC) in San Jose, California on June 3, 2019.

It's important to note that Cook didn't refute any of the facts in the Journal's story, and the paper told NBC News that it stands by its reporting. Plus, the carefully worded response was nowhere near as strong as when Cook called for a full retraction of Bloomberg's "Big Hack" story last year.

But Cook still had to go on the offensive.

In the Journal story, Cook and his COO Jeff Williams, who will now run Apple's design team, came off as operations nerds who have steered Apple away from focusing on mind-blowing products. Instead, they were risking everything that made the company so successful during Apple's rapid rise last decade thanks to its hot streak of hit products like the iPod, iPhone and iPad. The story made Ive look bad, but it made Cook look even worse.

"Mr. Ive grew frustrated as Apple's board became increasingly populated by directors with backgrounds in finance and operations rather than technology or other areas of the company's core business," the Journal's story said.

But today's Apple is a new kind of company. Not because it can't make popular products, but because it has reached such a size and scale that growth has to come from something other than a new kind of gadget. It's why Apple has been pushing so hard to sell its growth of services over the last couple years as it looks for new ways to squeeze more revenue out of its nearly 1 billion iPhone users.

Design and hardware are just one piece of a much larger puzzle at Apple as it explores new categories ranging from self-driving cars to artificial intelligence to subscriptions for streaming music and TV shows. Those projects may not appeal to someone of Ive's mindset, but they're fundamentally important to Apple's future.

Cook's response to the Journal's article wasn't so much of a defense of Ive's last few years at Apple as it was a defense of a new era at the company where it's focusing on a much bigger picture than how the next iPhone will look or what hardware category it'll break into next.

And what went unsaid in Cook's letter is just as important. Apple saw massive growth in its traditional hardware business under Cook's leadership, even while Ive was supposedly disconnected. He also saw the writing on the wall. The iPhone business couldn't grow forever, so he laid out several new avenues of growth for the company years before the iPhone peaked in sales. That's what an operations-focused executive is supposed to do. And it's what Apple needs in this new era.

Still, none of that means the classic, product focus at Apple is going away under Cook. And those concerned should look at the success of products Ive supposedly wasn't as involved in, like AirPods and the redesigned iPhone X.

"The design team is phenomenally talented," Cook wrote in the email to NBC News. "As [Ive] has said, they're stronger than ever, and I have complete confidence that they will thrive under Jeff, Evans and Alan's leadership. We know the truth, and we know the incredible things they're capable of doing. The projects they're working on will blow you away."

WATCH: Tim Cook says WSJ report on tensions with Jony Ive is 'absurd'