You have to read between the lines a bit. Their system is to store all metadata AND to record all phone calls. They can then go to a judge and get a warrant for calls that took place in the past, and (having previously recorded them) pull them up at will.
And metadata is a very broad term that encompases all data excluding the original. For example, "metadata" for a phone call would include electronically generated transcripts of the phone call. In theory (and probably practice) some algorithm scans these transcripts for keywords; on a match, they get a rubber stamp from a in-house judge, and then pass the records on to a human to do the real work.
Basically, someone figured out that you can use computers to wiretap the whole nation, and then did it. The whole constitution, legal framework, and morality be damned.