The document indicates the passenger tracking operation was a trial run of a powerful new software program CSEC was developing with help from its U.S. counterpart, the National Security Agency. In the document, CSEC called the new technologies "game-changing," and said they could be used for tracking "any target that makes occasional forays into other cities/regions."
The CBC notes early in the article that the spy agency:
is supposed to be collecting primarily foreign intelligence by intercepting overseas phone and internet traffic, and is prohibited by law from targeting Canadians or anyone in Canada without a judicial warrant.
Predictably, CSEC's chief is quoted saying that they aren't allowed to spy on Canadians, so therefore they don't. As observed by experts consulted for the story, that claim is equivalent to saying that they collect the data but we're to trust that they don't look at it.