Mark Zuckerberg is doing exactly what he promised Instagram and WhatsApp he wouldn't: messing with their independence by creating one system to rule them all.

The Facebook founder plans to bring the back ends of Messenger, WhatsApp and Instagram closer together with that of his own social network, as Facebook has now confirmed to the New York Times.

This consolidation may come with benefits for the billions of users involved, such as making it easier for anyone to send messages across the apps. But it's also the biggest sign yet that Zuckerberg is tightening his grip on services he once promised complete autonomy — and it comes on the heels of the Instagram and the WhatsApp founders exiting Facebook.

So at a time when trust in Facebook is at an all-time low, and when Silicon Valley is abuzz with rumors over bad blood between the founders, Facebook CEO is looking to wield even more control over its most prominent apps.

This is be a massive, multi-year undertaking for the social network. From the report (emphasis ours):

The move, described by four people involved in the effort, requires thousands of Facebook employees to reconfigure how WhatsApp, Instagram and Facebook Messenger function at their most basic levels. While all three services will continue operating as stand-alone apps, their underlying messaging infrastructure will be unified, the people said. Facebook plans to complete it by the end of this year or in early 2020 ...

Zuckerberg also ordered all of the apps to incorporate end-to-end encryption ... a significant step that protects messages from being viewed by anyone except the participants in the conversation. After the changes take effect, a Facebook user could send an encrypted message to someone who has only a WhatsApp account, for example. Currently, that isn’t possible because the apps are separate.

As of next year, then, Messenger, WhatsApp, and Instagram will run on the same infrastructure. Besides requiring years of engineering work, that could have unforeseen implications for the more than 2.5 billion people who use these services. It also raises questions of security and regulation.

The move also puts the departures of Instagram's Kevin Systrom and WhatsApp's Jan Koum into fresh light. Because this is the kind of thing Zuckerberg once pledged to them and their users that he had no intention of doing.

Back in 2012, when he first announced the $1 billion Instagram acquisition, Zuckerberg pledged to keep the photo sharing app independent. "We need to be mindful about keeping and building on Instagram’s strengths and features rather than just trying to integrate everything into Facebook," the CEO wrote in a statement.

Similarly, when Facebook acquired WhatsApp for $19 billion, the two companies were adamant that WhatsApp would remain independent from the social network.

"WhatsApp will remain autonomous and operate independently," founder Jan Koum wrote in a blog post at the time. "There would have been no partnership between our two companies if we had to compromise on the core principles that will always define our company, our vision and our product."

Systrom and Koum were both replaced with longtime Zuckerberg lieutenants. Both were said to have clashed with Zuckerberg on issues of independence. Namely, the founders' ability to run their services in isolation from the Facebook machine.

In the last year, as Instagram's growth has exploded, we've seen more Facebook tie-ins than ever before. The app has experimented with cross-platform notifications and placed prominent links back to Facebook in its app. Instagram's founders reportedly balked at Facebook removing references to Instagram when users posted photos from the photo sharing app back to Facebook.

Things are worse for WhatsApp. Not only are there ads and business messaging features now, but one of Koum's co-founders is on record as saying "I sold my users privacy."

WhatsApp and Instagram are still both technically independent services. Each has its own standalone app, and you can still use both without a Facebook account.

But for the people working on these services, a years-long project to merge their existing technical infrastructure with Facebook sends a clear message about their vaunted independence: those days are over.