The decision proper starts on page 12 of the PDF, and Chief Judge Gregory doesn't waste any time:

The question for this Court, distilled to its essential form, is whether the Constitution, as the Supreme Court declared in Ex parte Milligan, 71 U.S. (4 Wall.) 2, 120 (1866), remains “a law for rulers and people, equally in war and in peace.” And if so, whether it protects Plaintiffs’ right to challenge an Executive Order that in text speaks with vague words of national security, but in context drips with religious intolerance, animus, and discrimination.

By way of background, this is a challenge to Trump's second executive order trying to ban refugees from seven majority-Muslin countries. The first was blocked by the Ninth Circuit, and so Trump went back to the drawing board. But not for long enough, apparently. The second order tried to provide more justification by talking about how all the countries were "state sponsors of terrorism" and citing a couple of terrorist attempts by people from some of the countries named. It also did not prevent entry by people who had e.g. lawful permanent residency.

So after laying this out, things get quite interesting. The court cites Trump's repeated statements as a candidate that we should categorically ban Muslims from entering the country. Trump is then noted to say in an interview (after the constitutionality of banning people based on religion was questioned), "so you call it territories" (meaning the ban should be rephrased to be country-based rather than religion-based).

After discussing standing (i.e. whether the people suing have an actual injury related to the executive order), the court gets into the meat of the issue: whether the executive order is an unconstitutional under the Establishment Clause of the First Amendment.

The analysis goes like this. The Executive Branch has wide latitude to determine immigration policy, but still has to use that discretion in a constitutionally-permissible way. More specifically, courts have to defer to the president's immigration decisions unless they were made in bad faith.

This is significant, since the Fourth Circuit then goes on to basically say that Trump has been dishonest. The majority says that since it's clear that the reasons put forth by the administration (national security, mainly) were not made in good faith, the court does not have to defer to them. This in turn allows the majority to "look behind" the stated reasons, and try to evaluate what the real reason for the decision was. And, more importantly, whether that reason is secular or amounts to the government trying to favor one religion over another.

Looking at the facts in this light, the court concludes that the transition in Trump's language from outright saying he wanted to ban Muslims to making it based on country was pretextual, and done solely to avoid any constitutional issues:

These statements, taken together, provide direct, specific evidence of what motivated both EO-1 and EO-2: President Trump’s desire to exclude Muslims from the United States. The statements also reveal President Trump’s intended means of effectuating the ban: by targeting majority-Muslim nations instead of Muslims explicitly.

[...]

We need not probe anyone’s heart of hearts to discover the purpose of EO-2, for President Trump and his aides explained it on numerous occasions and in no uncertain terms.

In refuting the government's argument that the purpose is based on security, the Court cites two things: first, the fact that Trump didn't consult with anyone prior to issuing the first executive order, and second, that Homeland Security had concluded internally that such a ban would not be effective.

Finishing up, the Court dismisses the government's argument that national security can trump judicial review, finding that this is both inconsistent with the Constitution and that, in this case, it's an "ad hoc, secondary justification" for the action.

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Some commentators have described the degree to which the court basically called the president dishonest as extraordinary.

There's another thing going on with the opinion too: it's basically being written for Justice Kennedy. The majority on the Fourth Circuit knows that the case will be appealed to the Supreme Court, who may very well grant review. If so, it's likely to be Justice Kennedy that swings the case one way or the other, and so the majority tried very hard to cite to Justice Kennedy's opinions wherever possible.