A long-standing challenge is designing multi-scale structures with good connectivity between cells while optimizing each cell to reach close to the theoretical performance limit. We propose a new method for direct multi-scale topology optimization using neural networks. Our approach focuses on inverse homogenization that seamlessly maintains compatibility across neighboring microstructure cells. Our approach consists of a topology neural network that optimizes the microstructure shape and distribution across the design domain as a continuous field. Each microstructure cell is optimized based on a specified elasticity tensor that also accommodates in-plane rotations. The neural network takes as input the local coordinates within a cell to represent the density distribution within a cell, as well as the global coordinates of each cell to design spatially varying microstructure cells. As such, our approach models an n-dimensional multi-scale optimization problem as a 2n-dimensional inverse homogenization problem using neural networks. During the inverse homogenization of each unit cell, we extend the boundary of each cell by scaling the input coordinates such that the boundaries of neighboring cells are combined. Inverse homogenization on the combined cell improves connectivity. We demonstrate our method through the design and optimization of graded multi-scale structures.