There are four things to understand about the indictment.
1. The official story is that Bhutto was killed by the Pakistani Taliban. But a 2010 U.N. investigation raised serious suspicions about the roles of the Pakistani government and military in her death. It accused Musharraf's government of "inexcusable" failures to provide Bhutto with sufficient security and documented what it said was a cover-up by the military and its shadowy Inter-Services Intelligence agency. It stopped short, though, of implicating Musharraf himself.
2. The case against Musharraf seems to boil down, according to the New York Times, to two pieces of information, both of which come from the same person, a Washington lobbyist named Mark Siegel who was friendly with Bhutto. Siegel says that Musharraf threatened Bhutto in a phone call two months before her death. He also says that Bhutto once sent him an e-mail in which she said that if she were killed, it would probably be the work of Musharraf, along with another political rival and two military intelligence officials.
3. Pakistani courts have moved aggressively against Musharraf since he returned to Pakistan a year ago for what he hoped would be a political comeback. So there's certainly a political dimension to this. He was barred from running for office in April, then arrested three days later for abuses of power during his rule. In June, the current prime minister ordered officials to investigate possible treason charges.
4. On Monday, the lead U.N. investigator in Bhutto's death, Heraldo Muñoz, published an excerpt from his forthcoming book on the case, in Foreign Affairs. Here's what he writes about his look into Musharraf's possible involvement (my emphasis added):
Others believe that Musharraf was behind the murder. Bhutto had emerged as a threat to his government as she returned to Pakistan, making accusations about election rigging and the dangers of martial law along the way. And Bhutto herself had sent an e-mail to journalist Wolf Blitzer -- through a friend -- that was to be released only if she were killed, which affirmed that she would “hold Musharraf responsible” for her death because she had been “made to feel insecure by his [Musharraf’s] minions.”Further, there is evidence that Musharraf was increasingly angry at Bhutto for criticizing his regime so severely after having engaged in negotiations to secure a deal with him. In an interview only days before her death, Musharraf evidenced his acrimony toward her, complaining that, although there were “many things” he had negotiated with her, those agreements “[had] been violated.” Seeming to resent U.S. and British pressure to accept Bhutto as an ally, Musharraf said, with undisguised sarcasm, “It appears in the West that if a person speaks good English, it’s very good. A person who doesn’t know good English is quite unpopular in the West. And if he or she happens to be good-looking, then it’s better.”But all that does not constitute proof of culpability. Even Bhutto, despite her e-mail pointing a finger at Musharraf, probably did not believe that Musharraf wanted her dead -- only that some people around him did.
Muñoz did argue that Musharraf bears some "political and moral responsibility in the assassination," in part because he did not provide her with sufficient security, possibly for political reasons or to to pressure her to cooperate with him more. Still, he concluded, "We will probably never know with full certainty who killed Bhutto."