Most of the mess is because of the lack of organisation. The tools are spread all over the place instead of resting at their respective spots and in their boxes or the storage boxes are not stacked properly and are placed haphazardly. All this can go away if you organise properly and half the clutter will be gone before you know it.
Know What You Need
There are going to be a million things in your garage. Make a note of what you need and what you do not need, whatever is not required must be put away separately and arrange the rest of the stuff. Often you are going to find a huge amount of supplies that are of no use to you and have been taking space in the garage for years.
Once you have all that you do not need out, throw it away. It belongs to the trash so make the right move. In case these products are usable, either put them on sale via garage sale or simply put up a sign that says that anyone can take whatever they need from the pile. With people loving freebies, the stuff will soon be out and someone else will be messing up their garage for no reason.
If you do not maintain your garage, the mess will come back within a few weeks. That is far from ideal so make sure that everything sits in its designated space and you keep on making corrections to small issues such as out of order boxes. Taking a few minutes every once in a while will stop you from having to do the same exercise over and over again.