“A great new deal.” That is how UK prime minister Boris Johnson greeted the reworked withdrawal agreement and expanded political declaration, published on Thursday morning.

But it is not clear if this Brexit deal will be approved by the UK parliament, and while the revised political declaration on the future relationship says terms and conditions will be set out for the UK’s participation in EU programmes in science, innovation and education, this all has to be negotiated after the UK’s departure, meaning the uncertainty goes on for researchers.

Against that backdrop, here is a summary of how things stand.

First, whatever the outcome, UK researchers will still take part in most of the current research programme, Horizon 2020.

An analysis prepared by the UK government states that, under current rules, the UK post-Brexit would be allowed to take part in “calls open to third country participation.”

But pending agreement of the terms for future participation, UK-based researchers will no longer able to apply for three major EU funding programmes: the European Research Council (ERC), some parts of the Marie Sklodowska-Curie fellowship programme and the SME Instrument. That is because EU rules say scientists applying for these competitions must be based at host institutions that are legal entities in the EU or associated countries.

In a no-deal scenario, the UK would also no longer be able to access some space and security projects that only allow participants from EU countries, nor would it be allowed to participate in the Fast Track to Innovation programme.

The draft Brexit divorce deal drawn up last year – which was voted down by the UK parliament three times – stated that the UK would retain all the rights it currently has for a 21-month transition period – so long as the deal was approved by the UK parliament and the EU 27 member states.

The UK government has said if it cannot strike a new deal with Brussels, it will underwrite Horizon 2020 funding for all existing and future successful UK bids (those submitted from now until the end of 2020). The guarantee would cover the lifetime of projects, even if they extend beyond 2020. The offer improves upon the one made by the government in 2016, when it proposed to pay for successful submissions made before 29 March 2019. The government also says that it would continue to provide funding for its share of costs in the EU-funded Joint European Torus, the nuclear fusion experimental site based in the UK, until the end of 2020.

What kind of science relationship can the EU and UK have in the future?

Once outside the EU, the UK will have to completely renegotiate its access to EU research programmes. The UK government is committed to striking a new deal with the EU for the next research programme, Horizon Europe, starting in 2021, and the revised political declaration appears to give support for this.

Its most recent Brexit strategy white paper says the UK also wants to be a part of the Euratom research programme, the Joint European Torus, and the International Thermonuclear Experimental Reactor fusion project. However, it wants to have an “appropriate level of influence on the shape of the programme” in line with its financial contribution.

What does the EU want?

Whatever the warm words in the political declaration, the EU has not given the UK any firm guarantees about the shape of the science relationship after a Brexit transition period. However, the European Commission’s proposal for Horizon Europe contains the outline of a workable future relationship, with the UK as an associate member, providing the country with rights on a par with member states. The EU would like to open up Horizon Europe to greater participation from foreign countries. International participation in Horizon 2020 fell in comparison with the previous Framework Programme 7, in part because the EU changed the funding rules for countries including Brazil, Russia, India, China and Mexico.

What if there is no deal?

In an emergency measure to ease the disruption of a no-deal Brexit, Brussels earlier this year agreed that UK organisations could be eligible for EU science funding for the last two months of 2019, even if the country leaves without a deal on October 31. The European Parliament’s budget committee has improved on this offer, by voting this week to make EU funds available to UK researchers during 2020. The proposal, which is still to be approved by the full assembly, would make it possible to continue payments to UK beneficiaries throughout 2020, provided the UK continues to pay its EU contributions and accepts the necessary controls and audits. The EU has suggested that, in general under a no deal scenario, UK participants would continue to be eligible to take part in EU calls open to third country participation. However, the UK is warning researchers that the European Commission may terminate grants after Brexit for participants of a programme that is not open to third country participation.

What preparations are being made for a no-deal?

Recipients of Horizon 2020 funding in the UK are being asked to provide data to the public funding agency, UK Research and Innovation (UKRI), in order to prepare the underwrite guarantee. If the guarantee is required, UKRI will contact UK beneficiaries directly with information on the next steps they need to take to access funding. Organisations in EU countries who are part of a consortium with UK participants do not need to register with UKRI. Meanwhile, the UK government is considering replacements for ERC and Marie Curie programmes after Brexit.

What’s the money at stake?

For the UK, there’s a lot of money in the balance. The numbers brook little argument: between 2007 and 2013, the UK put €5.4 billion into the EU research pot and took out around €8.8 billion. European grants provide about 12 per cent of UK universities’ research income, for some institutions, they make up a much bigger share. Universities, as well as companies in research-driven industries like tech, aerospace and pharmaceuticals, are worried about losing access to EU research funding, and have established Brexit mitigation groups, amid signs that the UK might already be missing out on EU research funds.

Are there other ways UK entities could access EU funding in the future?

UK entities are exploring new forms of legal alliances as another way around funding uncertainties. The rules of ERC funding, for example, state that grant recipients must spend at least 50 per cent of their time at a host institute in the EU or associated country. UK institutions with outposts on the continent, then, could conceivably continue to access ERC grants, even in the case of a hard Brexit. UK-European alliances are sprouting up. For example, Imperial College London has signed a partnership with the Technical University of Munich to create academic posts jointly recruited and shared by the UK and German universities. Last year Imperial struck a similar deal with France's National Centre for Scientific Research to co-fund a maths laboratory in London, which will allow its UK mathematicians to have the same access to EU funding as French staff.

What happens next?

There are four scenarios: the UK government passes a Brexit divorce plan into law, it obtains another extension from the EU, it leaves without a deal, or it cancels Brexit. The focus now switches to the vote in the UK parliament. If the deal is passed, the UK will cease to be an EU member on midnight of October 31. If the prime minister cannot sell the deal to MPs, there will either be a request to Brussels to postpone Brexit day (for a second time) or the UK will crash out of the bloc without a deal. If a deal is not agreed between the UK and EU by late October, and MPs don't vote in favour of leaving with no deal, then the prime minister will be legally obliged to ask the EU for a Brexit delay until January 31. With the clock ticking, and any agreement needing approval of 27 member state governments and the European Parliament, time could simply run out. The UK may also hold a general election, and pressure for a second referendum or scrapping Brexit altogether could intensify.