Then Microsoft completely altered Skype's design (from supernode/P2P to client-server) making it cost a LOT more to maintain while offering no obvious advantages, which more or less confirmed it.
Quote from Microsoft PR on the change:
As part of our ongoing commitment to continually improve the Skype user experience, we developed supernodes which can be located on dedicated servers within secure datacentres. This has not changed the underlying nature of Skype’s peer-to-peer (P2P) architecture, in which supernodes simply allow users to find one another (calls do not pass through supernodes). We believe this approach has immediate performance, scalability and availability benefits for the hundreds of millions of users that make up the Skype community.
Here's a more conventional theory why they bought Skype. Around 2010, Microsoft is already moving toward a huge investment in mobile, where they've been completely blindsided by the staggering growth of iOS and Android. Their investment in Bing has not really paid off, and fighting Google on search has arguably been a distraction while this new-fangled iPad is about to destroy their entire PC market.
One major gap for their mobile strategy is a messaging platform. Windows Live Messenger capped out and is on the decline. They can build a new platform from scratch, but Windows Phone needs a tool that drives preference over iOS or Android. I'm not sure what their plan A was before Skype became available to buy, but it made sense as a plan B when it was for sale. With over half a billion users, it starts to look like a $10 CPA for customers.
Mobile also helps explain the shift toward client-server (as questioned by UnoriginalGuy below). If you had used Skype for mobile before, you'd know that it was basically a battery testing app. I haven't touched Skype much in the past year, but I think it's clearly improved.
Skype's business fundamentals aren't doing half-bad either: http://www.fool.com/investing/general/2013/02/15/still-think...
I don't know anything about what happened, but Microsoft must be one of the easiest companies to send a gift in a hidden way. Lets say the NSA bought Windows Vista upgrade licenses for a couple of million servers, then upgraded them to Windows 7 and form there to Windows 8, instead of doing what sane people do (upgrade from XP to a mix of Windows 7 and Linux). If you also upgrade SQL Server, Active Directory, etc, frequently and buy copious amounts of Remote Desktop licenses, I bet you could get the bill into the billions. And you don't even have to install that software, or even download it from Microsoft's servers.
Yes, it would raise suspicion that the NSA buys Windows licenses, even more so that they buy them at retail price, but I doubt that the auditors at the NSA are 100% independent from the NSA, so they would just (be ordered to) ignore it, and the NSA could route the buys through quite a few shadow companies, making it hard to spot anything suspicious for those working at Microsoft.
I know the advert is based around Internet Explorer rather than Microsoft as a wider organization, but that level of misleading advertising has to be in breach of trading standards (in the UK our trading standards laws are pretty strict).
The real question is whether they consider the PRISM leaks as evidence to challenge the tag line. Given the secrecy of the operation and Microsoft's denials, it the standards authorities might consider that evidence too much as hearsay to take definitive action.
I bet people won't think I'm so crazy now for posting before that the only reason Microsoft paid the incredible amount of $8.5 billion for Skype (and 2x as much as Google was willing to pay) for no good reason, is because they already knew they were going to make at least half of that money back from NSA:
http://www.theregister.co.uk/2009/02/12/nsa_offers_billions_...
Also this: "Microsoft's patent application for Legal Intercept was filed in 2009, well before the company's $8.5 billion purchase of Skype in May":
https://www.computerworld.com/s/article/9218002/Microsoft_se...
So they were already preparing to make it a spy technology before they even bought it. Microsoft bought Skype in May 2011. Look at the PRISM slide. They adopted PRISM for Skype in June 2011, a whole month after they bought it (in a hurry much?):
http://www.washingtonpost.com/wp-srv/special/politics/prism-...