24/06/2016 08:05 BST | Updated 25/06/2017 06:12 BST

Big Questions After Brexit

Stefan Wermuth / Reuters

The Prime Minister has triggered a Conservative Party leadership process, to establish who will lead the UK government through the challenges ahead. In the short term, this means we effectively have a caretaker government. The PM will remain in place and for uncontroversial issues, the cabinet nature of our government will come to the fore, with some progress being possible by consensus.

But any controversial decisions will be put off for the new Prime Minister, and his or her new Cabinet. This will cause difficulties, as a large backlog has built up in Whitehall over the referendum campaign. There is certainly no chance of a decision on issues like the expansion of airport capacity in the southeast (a decision that has been put off repeatedly for decades). However, the financial and performance pressures in services like the NHS may be more difficult to ignore.

The circumstances in which the Prime Minister announced his resignation are also important. The consensus from the Conservative Party that he could stay in office (even though many must have suspected he would resign) means the PM has enough authority to deal with any crisis that may come up. The UK still has a functioning government, even if it's not going to be a proactive one.

The big issue that the PM pushed to his successor was the timing and nature of the negotiations with Europe. When, and if, we trigger Article 50 (the formal process for leaving the European Union) as part of those negotiations, is a matter for another day. Indeed, the nature of the negotiations will itself be a matter of negotiation. The EU will, of course, have a huge say in how it negotiates with us, and will have its own political considerations that will determine its position.

And there are questions for Whitehall itself. The Civil Service is based on the notion that it is there to serve any government - you don't rise to senior positions within it unless you are prepared to do that. There is no doubt that the Civil Service will support the new Prime Minister and their Cabinet as fully as they have supported the incumbents.

But that does not mean things will be easy. Many of those on the Leave side have expressed suspicions about the role that the Civil Service has played. The Civil Service needs to start now in building up the skills it needs for the negotiations ahead. It will, quietly, make sure it has people in place who will have the trust of the Government as it moves forward. And it will think carefully about the structures it needs to put in place to allow the negotiations to work.

Finally, as David Cameron noted in his resignation statement, it is crucial that the UK government involves the devolved administrations in the negotiation process. Failure to reach consensus between the four governments could create serious constitutional problems, and would raise the likelihood of the Scottish Government pushing for a second independence referendum.

The process of choosing David Cameron's successor will take time and will undoubtedly cause further issues within government. The negotiations about how to negotiate will take time, and may themselves be difficult. And the negotiations themselves will take even more time. While the referendum result has brought some sudden clarity, interestingly there is quite a lot of time for people to prepare for the challenges ahead. Now we have to use that time wisely.

Julian McCrae is the deputy director of the Institute for Government

This blog first appeared on the IfG blog, and can be read here