Actually, they deliberately distanced themselves from telling an epic, theme-laden story with X due to it being their first HD game. The focus was on character builds and map exploration as well as experimenting with and implementing the tech skills needed for HD development.
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If it is connected, it would have been nice for it to have an epic, theme-laden main story like every Xeno game but Monolith made the right choice. Makes sense to develop a spin-off title where you can build the foundation for your future projects so it doesn't affect the story quality of the main series.