The resignation of Malta’s prime minister, Joseph Muscat, cannot come soon enough. The cloud hanging over the Maltese government in connection with the killing of the investigative journalist Daphne Caruana Galizia two years ago has grown much darker in the past few days. The EU, of which Malta is by far the smallest member, must now confront the political crisis within its borders head-on.

Manfred Weber, a German MEP and chair of the European parliament’s centre-right group, said on Thursday that the “assassination of a journalist with clear political links” should have “clear political consequences”, and an “urgent mission” is being dispatched. But, despite compelling evidence that Malta’s most famous reporter was the target of an assassination plot, EU leaders have so far been remarkably reticent. Questions about who was involved in the plot to blow up her car, and kill her, remain to be answered.

While three men – Alfred and George Degiorgio, and Vincent Muscat – were charged with carrying out the bombing in the summer, police are now probing who ordered them to do it. This week, new allegations led investigators to a businessman, Yorgen Fenech, who was arrested in the process of trying to leave Malta on his luxury yacht. Mr Fenech sought immunity from prosecution in exchange for information that he claimed would implicate Keith Schembri, Mr Muscat’s chief of staff, and two ministers in his Labour government.

Mr Schembri resigned, was questioned by police and released. The two ministers, Konrad Mizzi and Chris Cardona, also left their posts; they have not been arrested. The men deny criminal wrongdoing. But it is difficult for them to deny any connection to Ms Caruana Galizia, since her journalism revealed that Mr Schembri and Mr Mizzi were beneficiaries of secretive Panama shell companies.

These events are deeply troubling not only for Malta but for the EU. Malta, a secrecy jurisdiction with very lax banking controls, is known to be a conduit for dark money and also offers “golden passports”. If the rule of law is undermined on this island, the corruption could spread. Not long ago, it should be remembered, Mr Muscat thought he had a chance of replacing Donald Tusk as the president of the European council. The EU has previously invoked the article 7 process – which can lead to sanctions including, in the most serious cases, the withdrawal of voting rights – in response to attacks on the independent judiciary in Poland and Hungary. The Maltese opposition has previously called for similar measures to be taken against Malta. If the investigation does not now proceed smoothly, this would be a logical step.

Ms Caruana Galizia’s life’s work was exposing what was rotten on the island. While her life was brutally cut short, that work goes on.