President Trump wasn’t charged in the indictment that came down Thursday against the Trump Organization and its chief financial officer Allen Weisselberg.

But that doesn’t mean the case doesn’t include some potentially dangerous legal implications for the former president.

Court filings submitted by prosecutors alleged a pervasive scheme within the company to funnel off-the-books income to Weisselberg and other executives, suggesting that other Trump Organization leaders were involved. 

But the allegations unsealed this week represent only a small slice of conduct that prosecutors have been said to be investigating, raising the question of whether they will secure Weisselberg's cooperation in order to turn their sights on Trump himself.

If Manhattan District Attorney Cyrus Vance (D) does have bigger fish in mind, Weisselberg will have to weigh his loyalty towards the former president against the possibility of a conviction and a potential prison sentence.

“In any other investigation of a company, a CFO would be considered a major target,” said Daniel R. Alonso, a former chief assistant district attorney and federal prosecutor. “If a CFO is orchestrating the kind of financial fraud that's alleged in the indictment, that's a big deal. And the only question then is, who else was in on it? And here because of who the head of the company is, that question looms large.”

E. Danya Perry, a former federal prosecutor and deputy state attorney general in New York, says Weisselberg was a natural first target for Vance’s office because of his role in the company, his relationship with Trump and the evidence that prosecutors appear to have collected. 

“The DA's office would love to flip Weisselberg, there's no question about that,” Perry said. “He has described himself as the eyes and ears of the Trump Organization. He is the top lieutenant. He's got his fingerprints all over the organization's financials. And he was the other guy in the room with Donald Trump. So there's no question that they were going to scrutinize him extra hard to try and be as persuasive as possible to, shall we say, encourage his cooperation.”

Vance’s office filed 15 criminal charges against Weisselberg and the Trump Organization, including fraud, conspiracy and falsifying business records. If convicted, the executive could face up to 15 years in prison, though various sentencing factors would likely bring that number down, according to legal experts.

Both Weisselberg and the company pleaded not guilty on Thursday, and have denied wrongdoing.

“Today in New York City, violent crime continues to steadily rise to levels not seen in decades. Subway slashings, gun violence and hate crimes have become an every-day occurrence, with random shootings even happening in the middle of Times Square. Yet, instead of focusing on protecting the people of New York, the District Attorney has instead devoted countless resources for the sole purpose of targeting the former President,” a Trump Organization spokesperson said in a statement this week.

Trump added in his own statement, “The political Witch Hunt by the Radical Left Democrats, with New York now taking over the assignment, continues. It is dividing our Country like never before!”

According to the prosecutors’ court filings, Weisselberg was engaged in a scheme to funnel off-the-books income to himself and other executives at the company. The Trump Organization allegedly financed Weisselberg’s luxurious lifestyle, paying the rent for his Manhattan apartment, his living expenses, lease payments on his car and private school tuition for a relative.

Prosecutors say that Weisselberg received more than $1.7 million over a 15-year period that he never reported as taxable income and collected nearly $140,000 in tax refunds for which he didn’t qualify.

Adam Kaufmann, a former Manhattan assistant district attorney who supervised the office’s white collar criminal investigations, says that the type of charges brought against Weisselberg and the company are not uncommon for New York City’s local prosecutor, but he was struck by the level of organization that went into the conduct that the Trump Organization was allegedly involved in.

“It was really very systematic the way that they went about this, and just the way that there were so many different mechanisms,” Kaufmann said. “It wasn't just cash payments under the table, which would be more common.”

“To me, it just looks like there's almost an arrogance to it,” he added. “Like the rules don't apply.

Trump has not been charged with anything and there are still no signs of whether he could be facing a criminal case. But both Vance’s office and New York Attorney General Letitia James (D) have spent considerable resources over the past several years investigating the president and his businesses, and fighting him in court for his personal and business records.

The district attorney’s office obtained the former president’s tax returns earlier this year after a protracted legal battle over Trump’s lawsuit to block Vance’s subpoena.

Court filings and media reporting have indicated that the two offices are investigating widespread fraud and other financial crimes at the company, but the exact contours of the probe are still unknown.

Some of the conduct that’s said to be under investigation is whether Trump and his businesses inflated the value of assets in order to win favorable loans or attract investors.

Legal experts say that it’s usually important for a white-collar fraud prosecution to have a cooperator on the inside of a scheme who can help connect the dots for investigators and jurors.

Perry, the former deputy state attorney general, said it could be all the more critical for Vance’s office in any potential case against Trump in part because he is famously averse to using email or other written electronic communications that leave a paper trail on which prosecutors can build a case and prove intent.

“It's a good-faith defense to say, 'Well, they told me I could do this, they said this is how it's done,'” Perry said. “And when you're the CFO of a company, and you're seeing the whole paper trail, it's harder to make that argument, but it gets easier as you're a little removed from those transactions. And I have to believe that Trump is at least one step removed from them, so that's why to make that link and to draw the connection and to prove up specific intent, it's pretty useful, if not absolutely critical, to have a live witness.”

The fact that prosecutors indicted Weisselberg indicates that he has been unwilling to cooperate in the investigation. Perry says that it’s difficult to predict whether people will flip on alleged co-conspirators, but added that being under indictment adds significantly more pressure than merely being under threat of indictment.

“He may have a different calculus now than he did before Thursday,” Perry said. “It's hard to predict what any individual will do. I will only say from experience, I've seen a lot more hardened criminals than a 73-year-old accountant buckle under it then start cooperating once charges are actually filed.”

Kaufmann added that another looming question about Vance’s investigation is what and how much evidence prosecutors have collected so far.

“Of course the DA wants Weisselberg's cooperation,” Kaufmann said. “The question I continue to have is, do they need Weisselberg's cooperation? We just don't know.”