The Trump administration not only dislikes the European Union, it is out to destroy it. The trip by the US secretary of state, Mike Pompeo, to Europe last week was episode three of the onslaught, designed to play on east-west divisions within the EU. Episode one was Donald Trump’s 2017 Warsaw speech, infused with nativist nationalism. Episode two was Trump’s 2018 moves on tariffs, and his tearing up of key agreements such as the Iran nuclear deal and the Intermediate-range Nuclear Forces (INF) treaty. To which should be added his open encouragements to Brexiteers, and his decision to pull out of Syria. All of the above affect European (including British) interests in very concrete ways, unlike mere tweets or insults thrown at allies.

Europe is trying to put up a resistance. Angela Merkel, Trump’s favourite political target in the EU, received a standing ovation on Saturday at the annual Munich security conference for her speech on the virtues of multilateralism. But perhaps we have yet to fully fathom what the EU is dealing with in this new Trump era. The man now whispering into Trump’s ears is John Bolton, his national security adviser. His brand of anti-EU ideology was on full display during Pompeo’s tour of Budapest, Bratislava and Warsaw.

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Pompeo has done two significant things. First, he in effect took possession of this year’s 30th-anniversary celebrations of the fall of communism in eastern Europe by waxing lyrical on US closeness to nations that fought for their freedom – all the while giving a free pass to rightwing populist governments that the EU has put on notice for their democratic backsliding. Second, through his choice of destinations, Pompeo amplified divisions between countries formerly behind the iron curtain and those that weren’t. This astutely plays on sensitivities, manipulated by demagogues, that have marred the EU’s capacity to unite in recent years.

Some of it smacked of 2003 when, in the run-up to the Iraq invasion, the US defence secretary, Donald Rumsfeld, coined the terms “old Europe” (bad) and “new Europe” (good). But one big difference today is that the European project is struggling to keep afloat; back then optimists believed it would “run the 21st century”. An article Bolton penned in 2000 helps to bring the Trump strategy into sharper focus. Headlined “Should we take global governance seriously?”, it reads today like a roadmap of the Trump administration’s intent to destroy the EU. In it, Bolton lashes out at “globalists” who seek to tie nation states into a web of international norms and agreements that restrict sovereignty. He says a truly democratic mandate can only exist at the national level. Along the way, he hammers NGOs and civil society (“which sees itself as beyond national politics”) and the “limitless” breadth of multi- or supra-national institutions.The EU, he says, is “the leading source of substantive globalist policies”.

Bolton goes further: he identifies the EU as a threat to US interests (last year Trump called it “a foe”). “European elites” are “not content alone with transferring their own national sovereignty to Brussels, they have also decided, in effect, to transfer some of ours to worldwide institutions and norms, thus making the European Union a miniature precursor to global governance”. And he depicts the EU as “tinged with a discernable anti-Americanism”.

Facebook Twitter Pinterest Mike Pompeo and Viktor Orbán in Budapest last week. Photograph: Balazs Szecsodi/Hungarian Prime Minister’s Press Office/HANDOUT/EPA

Never mind that Trump has arguably done more to bolster anti-American sentiment in Europe than any other US leader. What this reveals is that conventional explanations often given for Trump’s attacks on the EU are only one part of the picture. Trump’s anger at the EU as a trading bloc, his tactics to boost US armament exports to the continent, as well as his personal aversion to Merkel, are but the translation of a wider ideological battle about global governance.

Beware of thinking Bolton’s 2000 writings are outdated. They will only appear so if you believe the Trump administration has no ideology whatsoever, only commercial interests. It’s true that it’s a bit of a stretch to think of Europe today as capable of challenging the US on the global stage: in comparison it is a military weakling, and has endured a decade of crises. Yet it embodies something Trump and Bolton detest. And some of its larger member states are now trying to stand up in ways that clearly irk the Trump team – as with the new mechanism to sidestep sanctions against Iran.

Meanwhile, though liberal central Europeans may hope for positive US engagement in the region – such as Pompeo’s promise to support an “independent media”, and Nato deployments facing Russia – that glosses over what I’d describe as the “newspeak” contained in last week’s visit. Words such as “freedom” and “independence” flowed from Pompeo’s mouth as he paid tribute to those who broke away from communist dictatorship. But there was no mention that the EU helped to anchor democracy. The value-based dimension of the EU is arguably stronger than that of Nato – an alliance that for years included authoritarians (think Portugal’s Salazar regime, and the Greek colonels in power in the 1960s), and does again with Recep Tayyip Erdoğan’s Turkey.

Pompeo’s talk of freedom, above all, echoed Bolton’s thinking. “All Americans celebrate their own individual freedoms, and are at least well wishers for others around the world to enjoy the same freedoms,” Bolton noted in 2000. However, attacking the EU, he added that the “‘human rights’ rubric has been stretched in a variety of dimensions to become an important component of globalists’ effort to constrain and embarrass the independent exercise of both judicial and political authority by nation-states”. Today, that thinking fits perfectly with rightwing populists in Warsaw and Budapest who complain about the EU’s response to their curtailing of independent judges and media.

With less than 100 days before the European parliament election, Pompeo had dinner in Hungary with its prime minister, Viktor Orbán, who wants to redraw Europe’s political map to suit his vision of “illiberal democracy”. They may have disagreed on Russia, and it’s true Pompeo did also meet NGO representatives in Budapest, but there was little sign of divergence with Orbán over values. It’s true also that Pompeo visited Slovakia, whose government thinks of itself as a constructive member of the EU, not a disruptor. But this was possibly aimed at drawing Slovakia deeper into the embrace of European illiberals, not the other way around.

Pompeo’s visit was a vindication of the enemies of a values-based EU, and another attack on the EU’s very existence. Postwar Europe was able to build itself up as a collective project thanks to US protection and financial support. Today the EU is the target of multi-faceted political offensives from both Washington and Moscow, not just because of what it does, but what it is. The earlier Europeans take stock of this, the better.

• Natalie Nougayrède is a Guardian columnist