The American people have the right to be free from unreasonable searches. It's a constitutional right that stems from the Fourth Amendment that is meant to protect the people from the government. Microsoft has been fighting since April to stop the government from searching users' cloud storage without providing notice to the searched user. In the most recent filing, Microsoft has found unusual allies in not only Google and Apple, but also Amazon, BP, Fox News, Delta, the EFF, and even the US Chamber of Commerce.
Basically, the issue focuses on the government's ability to obtain not just a search warrant to search through a user's files stored on the cloud, but also a gag order which prevents the company providing the cloud storage from notifying the user that the search will occur or has occurred.