Thomas Jefferson's only real plan for Native Americans was to try push them out of the lands that white settlers wanted, particularly if the Indians would not assimilate into white culture. While the Louisiana Purchase was not made with this goal in mind, it did give the United States a place to put the Indians if they needed to be pushed out of territories they occupied.
Jefferson had in mind to push Native Americans off to the west of the Mississippi River. This can be seen in the google.com link below. With the Louisiana Purchase, the US obtained a great deal of land west of the Mississippi. This meant that the US could now (as Jefferson planned) have a place to which to move Native Americans who were in the way of white progress.