Here in logical steps is the unavoidable answer:
(1) Due to whatever in history before 1776, the US founding fathers gave us the Constitution. Soon they gave us the Bill of Rights. In particular we have the Fourth Amendment.
(2) Congress, the FISA 'court', the Intelligence committees of Congress, the president, the NSA, etc. may have done this and that, but there are claims that the Constitution has been violated.
(3) Law suits are being brought claiming that the Constitution has been violated. Apparently there will be suits from Google, EFF, and the ACLU, and there's little to stop more suits from being brought. It appears that quite generally lots of lawyers will be burning midnight oil, word processing, filing cases, etc.
(4) Very likely some of these law suits will make it to the steps of the Supreme Court, be taken in by the court, studied, argued, and decided. If the Constitution has been violated as clearly and strongly as it is easy to guess from the recent news, then the court will likely strike down at least some of the laws that enabled the violations. Really, for this process, nothing can stop it now -- not the president, the NSA, the FISA court, Congress. People can argue this and that, that we need what the NSA has been doing or we don't, but still the Supreme Court will take this issue and address it.
(5) The founding fathers made sure that the Supreme Court was not just a bunch of kids playing tag on a playground. Instead the SCOTUS (Supreme Court of the US) is about as serious as anything in this solar system. The court is absolutely, positively 100% aware of the Constitution, their role in defending it, and threats to it. Arguments of short term expediency, the threats of Boston loser wackos with backpacks with pressure cookers, Jihaders with chembio in public places, or well funded efforts to sneak a nuke into a major US city will not be seen as repealing the Bill of Rights or even one comma in the Constitution. And the SCOTUS is just awash in power, both in principle and in practice, to strike down as unconstitutional whatever parts of the Patriot Act, the FISA court, etc. they conclude, with considerable study and wisdom, is appropriate.
The process of (1)-(5) has now started and will move forward "with all deliberate speed" which might be 1-2 years.
In simplest terms, the SCOTUS can, yes, understand the threats of terrorism but can understand with much greater concern the threats to the Constitution. The SCOTUS has no choice but to pay essentially all their attention just to the threats to the Constitution.
It's the process: The Executive branch is supposed to follow the laws and, really, can't change the laws. If the laws are too limiting for the important work of the Executive branch, then have Congress pass some new laws. We did that. If the new laws are unconstitutional, then bring suits before the SCOTUS to have the unconstitutional laws struck down. We're now in the process of doing just that. The SCOTUS has to protect the Constitution and can't change it. If the Constitution needs changing, then that's 2/3rds of the House, 2/3rds of the Senate, and 3/4ths of the states.
So, in 1-2 years we will know. The smart money is on the Constitution coming out whole. And the chances of an amendment to the Constitution are as usual from slim to none.
So, where will the SCOTUS defending the Constitution leave Congress, the Executive branch, the NSA, the FBI, local police, etc.? They will have to put their thinking caps on and find ways to protect the US from the Jihaders within the Constitution. Or the Executive branch will find more ways to violate laws and/or the Constitution, and then there may be more leaks, law suits, etc.
Whatever, and it may take time, in this mud wrestling the Constitution stands to come out whole. Thank you founding fathers.
Did the founding fathers see this coming? Absolutely. Been there; done that; got the T-shirt, 200+ years ago.
Or, we need to defend the US. One of the best parts of the US is the Constitution. So, it is logically impossible to defend the US and trash the Constitution. Instead, in defending the US, it is in particular necessary to defend the Constitution. For also defending the rest of the US, that's a problem we have to work to solve; I have no doubt at all we can solve it.
In simple terms, the problem is not finding ways within the Constitution to stop the Jihaders. Instead, the problem is stopping intellectually lazy, empire building bureaucrats and CYA politicians from using the Jihader threat as an excuse to trash the Constitution, build empires, and CYA.