Microsoft filed the lawsuit back in 2016 to fight for its customers' right to know if and when the government asks for their data. See, requests for data stored in the cloud come with gag orders that have no expiration date, and Redmond argued that it violates people's First and Fourth Amendment's rights. Judge Robart did drop Microsoft's Fourth Amendment argument, but he mentioned that the company can bring it up again when it reaches higher courts:

"Some of Microsoft's customers will be practically unable to vindicate their own Fourth Amendment rights.

... This conundrum, however, is not unique to this case; it is also true of the victim of an unreasonable search in a stranger's home. See Alderman, 394 U.S. at 134. The source of the court's conclusion is thus the product of established and binding precedent, which precludes the court from allowing Microsoft to vindicate Fourth Amendment rights that belong to its customers. This court cannot faithfully reconcile the broad language of those cases and Microsoft's theory of Fourth Amendment standing on the facts of this case; that task is more properly left to higher courts."

When authorities want to access documents and other physical data, they have to notify people that they asked for their private information or that they seized their property. Since perpetual gag orders prevent the company from telling their customers the truth, it expands the government's ability to conduct covert investigations. That's the reason tech companies fight gag orders in court and why Microsoft will continue pursuing this lawsuit.

Microsoft general counsel Brad Smith told Ars Technica: