The organization behind Kony 2012 - Invisible Children Inc.- is an extremely shady nonprofit that has been called "misleading," "naive," and "dangerous" by a Yale political science professor, and has been accused by Foreign Affairs of "manipulat[ing] facts for strategic purposes." They have also been criticized by the Better Business Bureau for refusing to provide information necessary to determine if IC meets the Bureau's standards.
Additionally, IC has a low two-star rating in accountability from Charity Navigator because they won't let their financials be independently audited. That's not a good thing. In fact, it's a very bad thing, and should make you immediately pause and reflect on where the money you're sending them is going.
By IC's own admission, only 31% of all the funds they receive go toward actually helping anyone [pdf]. The rest go to line the pockets of the three people in charge of the organization, to pay for their travel expenses (over $1 million in the last year alone) and to fund their filmmaking business (also over a million) - which is quite an effective way to make more money, as clearly illustrated by the fact that so many can't seem to stop forwarding their well-engineered emotional blackmail to everyone they've ever known.
And as far as what they do with that money:
The group is in favour of direct military intervention, and their money supports the Ugandan government's army and various other military forces. Here's a photo of the founders of Invisible Children posing with weapons and personnel of the Sudan People's Liberation Army. Both the Ugandan army and Sudan People's Liberation Army are riddled with accusations of rape and looting, but Invisible Children defends them, arguing that the Ugandan army is "better equipped than that of any of the other affected countries", although Kony is no longer active in Uganda and hasn't been since 2006 by their own admission. These books each refer to the rape and sexual assault that are perennial issues with the UPDF, the military group Invisible Children is defending.
And to add - Conned 2012: Joseph Kony Is/Was A CIA Contractor - According to former European MP, journalist, and author Richard Cottrell, the Lord Resistance Army is backed by the CIA and Mossad.
The author of the blog aangirfan writes: "In Uganda, Joseph Kony is the leader of the Lord's Resistance Army, 'which is a US and Mossad-backed guerilla force.'" He quotes Richard Cottrell, a former European MP, journalist, and author of the book, "Gladio: NATO’s Dagger At The Heart of Europe," who wrote in an article in October 2011 called, "African ping pong: US plays both sides in Uganda":
"The Lord’s Resistance Army (LRA) rampaging around Uganda is nothing more than a US and Mossad-backed guerilla force.