The argument on fisheries was as follows. The pro-Western Sahara side argued that the territory is occupied and therefore subject to the rules of international humanitarian law (as was eg Iraq under the Coalition Provisional Authority in 2003-04). Its resources, including off-shore resources, must therefore be exploited only with the consent of the local population, and for their benefit. The EU should not therefore be in the business of making agreements that treat the Western Sahara as if it was any part of Morocco.
EU officials who I picked this up with would reply that they were agnostic about the Western Sahara's status, and it was Morocco's business, not the EU's, how and where the fisheries agreement would be applied. This later got modified to acknowledging that some of the fisheries profits needed to benefit local people, but with no explicit mention of Western Sahara in the legal documents themselves. This of course was driven by the (entirely real) needs of Spanish fishermen to continue fishing those waters, which had been part of the understanding on which Spain joined the EU in 1985, and the political closeness between Moroccan and French political elites.
The counter-argument is that the EU and its treaties should be subject to international law, and that the fisheries agreement clearly breached it. The problem was finding a legal means by which this can be done. We tried and failed to get the European Parliament to refer the question to the ECJ in 2011.
In 2015, the European Court of Justice ruled that a different EU-Morocco agreement on agriculture was illegal because it included the Western Sahara as part of Morocco. The EU succeeded on appeal in having the agreement reinstated, but only insofar is it did not apply to Western Sahara. Those actions were brought by the Polisario Front, the liberation movement of Western Sahara. A substantial part of the proceedings revolved around whether or not the Polisario Front, which obviously is not itself an EU-based organisation, should have the right to appear in the proceedings at all.
Last week the ECJ's Advocate-General, the official whose job it is to lay out the legal principles of each case to the judges and report on the likely ruling, published his opinion on the fisheries agreement. It's pretty hard-hitting. He says,
Since the assertion of Moroccan sovereignty over Western Sahara is the result of a breach of the right of the people of Western Sahara to self-determination, the Advocate General concludes that the EU has failed to fulfil its obligation not to recognise the illegal situation resulting from the breach, by Morocco, of the right of the people of Western Sahara to self-determination and also not to render aid or assistance in maintaining that situation.(Full opinion here, full of juicy lawyerly details.) The Court may (and sometimes does) choose to go in a different direction from the Advocate-General, but they are all reading the same texts and are therefore likely to come to the same conclusion.
This matters because Morocco's policy for forty years has been one of normalising the status quo and the illegal occupation of their southern neighbours. The EU, by not differentiating between Morocco and Western Sahara in its international agreements, was colluding in that process. The ECJ has now said, twice, that that must stop.
Total congratulations to John Gurr and his colleagues in Western Sahara Campaign UK, a tiny NGO headquartered in Cardiff, which found a legal path to take this case through the British system and up to the ECJ, shaking the foundations of the EU's policy in its neighbourhood. It is a proof of Margaret Mead's dictum: "Never doubt that a small group of thoughtful, committed, citizens can change the world. Indeed, it is the only thing that ever has."
(I should add that these days I am a mere observer of this question; I haven’t worked on the Western Sahara issue since 2014.)