Special counsel Robert Mueller's recent court filing seems to contain a very clear message to President Donald Trump and his allies: This investigation is bigger and goes far deeper than you think.

That was MSNBC's Chris Hayes' takeaway, as he discussed in Thursday's episode of "All In."

Hayes argued that despite people like Rudy Giuliani and Vice President Mike Pence suggesting that Mueller should wrap up his investigation into Trump's campaign and Russia's interference in the 2016 election, the new document, filed in response to media outlets' request for documents, suggests the investigation is nowhere close to done.

"The Special Counsel's investigation is not a closed matter, but an ongoing criminal investigation with multiple lines of non-public inquiry," the filing says, indicating that there are many facets of the probe that are not well-understood by the public. "Many aspects of the investigation are factually and legally interconnected: they involve overlapping courses of conduct, relationships, and events and rely on similar sources, methods, and techniques."

This suggests that, despite the fact that many of presidents defenders have repeatedly pointed out that none of the public indictments made public so far by the investigation directly allege "collusion" between the Trump campaign and Russia, Mueller may still be keeping these aspects of the inquiry under wraps for now.

Another section suggests that even those implicated in public indictments may be involved in other matters of interest.

It continues: "Here, the government's warrant applications and related materials, including those that relate to people who have already been charged or pleaded guilty, are part of the Special Counsel's ongoing investigation. Disclosure of those materials could reveal sources, methods, factual and legal theories, and lines of investigation extending beyond the charged conduct."

Watch the clip below: