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Besides mining for resources, Minister Tua suggests in Star Wars Rebels: The Siege of Lothal that there is a secretive reason for the Empire being on Lothal.

"No...There is another reason, known only to a few, and ordered by the Emperor, himself."

What is the "true reason" the Empire are on Lothal?

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Unknown. However, there is a very good candidate.

Possibly the presence of Kyber crystals

As we know from Ultimate Star Wars, the Death Star used a Kyber crystal in its superlaser. The protagonists of Rebels have seen other signs of Death Star construction.

The Rebels on Lothal sought to prevent a Kyber crystal shipment (probably from Lothal) from reaching the Empire.

From "Breaking Ranks" (Star Wars: Rebels 1x04):

HERA: What's the alternative? Do you want to stop that Kyber shipment or not? You know what the Empire could do with that crystal.

KANAN: Nothing good.

and further

HERA: And we'll only get one shot at this.

KANAN: The Kyber crystal resonates with the Force.

This suggests that Kyber crystals are mined on Lothal, which indicates that they may be supplying them as material for the Death Star.

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In the season 4 episodes "Wolves and a Door" and "A World Between Worlds," it is revealed that the Emperor ordered the base on Lothal in order to access its Jedi Temple. The Lothal Jedi Temple is one of the gateways to the World Between Worlds, a mystical plane within the Force that has various pathways to different areas of time and space.

According to the Wookieepedia article on the World Between Worlds:

Darth Sidious, ruler of the Galactic Empire, sought to enter the world between worlds, as gaining access would give him unimaginable power, and as Minister Veris Hydan believed, control of the universe.

This explains why Palpatine ordered the base on Lothal, because he believes it would give him unlimited power.

Additionally, the TIE Defender was developed exclusively on Lothal. Cheaper and possibly more efficient than funding the Death Star, Grand Admiral Thrawn utilized Lothal's extensive fuel depots to fuel the project he developed. Several of the prototype defenders were built, but Governor Arihnda Pryce's destruction of the fuel depots forced the project to be shut down indefinitely.

Wookieepedia article on World between worlds

Wookieepedia article on TIE Defender

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  • @Valorum True, I'll add something about the TIE Defenders. – Donatello Swansino Mar 28 '20 at 23:53
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The repeated references to Lothal's significance to the Empire as a site for mining, the fact that there's a significant hidden Jedi temple on the planet and the fact that under said Jedi Temple is a large cavern where you can collect Kyber crystals would all strongly suggest that the Empire is mining crystals for use in some sort of gigantic super-weapon that uses Kyber crystals as a key component.

The fact that they're taking lots of extra minerals out of the ground (which can then be used to make starships) may well be secondary to their original objective.

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