He left Sam behind in the bunker to visit his mom (and unintentionally meet up with Nick), and he was doting enough that it set off alarms for Mary.
Intending to lock himself inside, Dean went on a bit of a farewell tour before leaving everything behind.
He had to build a special box that would theoretically contain Michael.
Going off of the information from Billie, Dean came up with a way to take Michael out of the equation, but it would unfortunately remove him from the equation as well.