People who support the Multiple Deposition Theory believe that water containing “silica”, or the basic ingredient for Lake Superior agates leaked in from the cracks. Over a period of time the silica deposited layers over layers, usually until the vesicle filled up, and then the moisture escaped back through the cracks into the open air. Their evidence for this is the visible layers that you see in a Lake Superior agate.
On the other hand, believers of the Single-Gel Theory say that there is a single gel that already has all of the minerals needed inside of the vesicle, and it separates out into bands as soon as the cracks to the outside are closed. The bands are determined by impurities, or other minerals that are present in the gel. These impurities control when an old band stops and a new band starts. Their evidence for this is that if the appearance of the agate was based on the environment, all agates in the similar vicinity would look alike, and that is not the case.
There is no one theory that holds the explanation to all varieties of Lake Superior agate, though. Now, back to the formation of Lake Superior agates.
A long while after the agates solidify in the vesicle, the basalt holding them inside breaks down and crumbles, very gradually letting the agates out. The reason that the Lake Superior agates did not crumble and the basalt host rock did is because silicon, the mineral agates are composed of, is a very strong mineral and it does not break down as easily as basalt.
Finally, beginning 30,000 about years ago, when many, many Lake Superior agates were sitting out in the open, the Ice Age’s glacier lobes began slowly passing through Minnesota and took the agates along for the ride. The thousands of years of glacier transport cracked and chipped the agates, and ultimately spread them out into waterways and open land across hundreds of hundreds of square miles.
In conclusion, the journey of the formation of the Lake Superior agate is an amazing, tremendous, beautiful thing, but it is not necessarily completely understood.