Apple Inc.’s (NASDAQ:AAPL) battle against a legal order requested by the government to provide a backdoor into Apple’s ecosystem is over. The U.S. Justice Department announced that it had succeeded in accessing the data on the San Bernardino shooter’s iPhone removing the need for Apple to step in. However, the resolution of the legal dispute brings above some questions regarding Apple’s security and how the FBI was finally able to crack the encryption.

With the end of Apple’s legal fight against the government, the notion that Apple’s security is good enough to withstand the resources of the U.S government (something that seemed plausible just a few days ago) has evaporated. The Government has reported that they have accessed the phone of the San Bernardino shooter and subsequently asked the federal judge in the case to vacate the order that asked Apple to aid the FBI into bypassing the encryption on the phone.

The Department of Justice has stated that the FBI is in the process of analyzing the data on the device and will do so strictly according to the standard procedures in such an investigation. Providing further details, the official revealed that the FBI would comprehensively study all the data at its disposal and was in the process of reviewing the shooter, Farook’s Facebook.

The government has stated that the data was obtained via a third party method recently shown to the FBI but refused to disclose the name of the party or elucidate what the method was. Apple responded to the development stating that the request for a back door from the FBI was unreasonable and should have never been made. Such a request would have set a dangerous precedent for the security of Apple users.

Apple reiterated its commitment to working with authorities but also promised users that it would continue to amp its security as Apple devices were now being targeted more vigorously with even more sophisticated methods.

The resolution of the case, however, raises some troubling questions regarding the security of user data. Firstly, if what the government says is true, there is a third party which has the techniques that allow access to data on Apple devices, a task that even the current administration did not seem to be up to despite its infinite resources.

The other more troubling possibility is that Apple might have secretly helped the government access the device. If this is true, it could mean that Apple secretly handed over a backdoor to the FBI to avoid a public debacle which would have been imminent if it had failed in its appeal against the legal order to help the FBI access the San Bernardino shooter’s device. There is currently no information to support such a view as yet, but it is a reasonable assumption considering the strength of Apple’s security. Either a third party helped the FBI crack into the iPhone device of the San Bernardino shooter as the DOJ says, or it was Apple that helped the FBI on the sly to make the case go away.