ANNAPOLIS — After weeks of intense negotiations, the Maryland General Assembly’s attempt to clean up the state’s medical-marijuana program came to an abrupt end Monday night in the final seconds of this year’s legislative session and ended the attempt to Extend Maryland Grower Cannabis Licenses.

The efforts to meld House and Senate bills into one measure that both chambers would accept went on all evening, with each house refusing to back down — until finally, just before midnight, the House Health and Government Operations Committee agreed to the Senate’s terms.

That included the many licenses for two firms that were unceremoniously bumped last summer from the list of companies approved for the first 15 licenses to grow cannabis for medical use in Maryland.

One of those companies, GTI Maryland, had plans to cultivate a crop in Washington County. They would have benefited tremendously from one of the Maryland Grower Cannabis Licenses.

As the clock ticked, the compromise came to the floor. A procedural vote was called, and the delegates agreed 84-51 to take a final vote on the measure for the evening.

But then several Republican lawmakers were asked to explain their votes. And they are permitted two minutes each to do so.

Sometimes knowing that other legislation is pending will encourage them to take their seats and get back to voting. But on Monday, there were not any major bills left and the clock ran out.

In the noise and chaos that usually accompanies the last hours of the session, there was some confusion over what had happened. Some thought the bill passed for Maryland Grower Cannabis Licenses; lobbyists for interested companies were texting their clients that they had won.

Del. Brett Wilson, R-Washington, at first was unsure whether the vote had been taken in time. When he realized the final vote had not gotten done, his frustration surfaced.

“If we better used our time earlier in the session, we wouldn’t have these messes at the end,” he said.

But a lot of time had been expended on the issue by lawmakers in both parties and in both chambers. Not all Republicans opposed the bill, and not all Democrats liked it.

By Monday, many thought the issue had devolved into a game of chicken between the House and Senate.

In remarks to reporters after the session ended, Gov. Larry Hogan attributed the failure to disagreements between House Speaker Michael E. Busch and Senate President Thomas V. Mike Miller over what should be included in the bill.

“We weren’t involved in that,” he said.

Since the bill did not pass, lawsuits filed by GTI and the other company, Maryland Cultivation and Processing LLC, which planned to grow medical marijuana in Frederick County, will likely go forward, said Sen. Andrew Serafini, R-Washington.

Serafini and Wilson had filed bills to reinstate those companies for Maryland Grower Cannabis Licenses, who initially scored 12th and eighth, respectively, on the list of companies eligible for the 15 available licenses.

But because of concerns about a lack of “geographic diversity” among licensees — two other firms won licenses to grow the crop in each county — they were replaced by lower-ranking firms that proposed cultivation in Prince George’s and Worcester counties.

The legislature first approved marijuana for medical use in 2014.

The final bill included Serafini’s and Wilson’s effort to get licenses for the companies.

It also addressed a third lawsuit, filed by Alternative Medicine Maryland, claiming the commission had not considered minorities when making its licensing choices.

The bill would have required a diversity study to be conducted before future licenses are added and reformed the licensing panel.

But it all fell apart as the clock struck 12, and now the issue will likely be decided in a courtroom.

Serafini said he believes GTI has a strong case and could win its lawsuit.