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In the final battle, Scarlet Witch pinned Thanos upon which he told Corvus Glaive to...

"Rain Fire!"

... which seemed to open fire like Gatling guns and nearly injured all parties fighting. However, it quickly shifts and started firing towards the clouds where Captain Marvel was emerging from.

Why did the Sanctuary II focus its attack on Captain Marvel?

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    A prior encounter is not required. 2018 Thanos knew of Tony Stark before he met him. By 2014 Captain Marvel would have been protecting planets for maybe two decades. Stories of her destruction of Ronan's ship and other activities would have gotten around. And some way might have been developed of detecting her approach. So a "Captain Marvel incoming!" warning on the bridge of Sanctuary II is within the realm of possibility. – nebogipfel May 24 '19 at 4:13
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    It's not even required for Thanos to know that Captain Marvel is a person. If you were on that ship, firing the guns, and you saw something blazing full of energy coming right at you like a missile, wouldn't you try to shoot it down? – Robyn May 24 '19 at 7:48
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    2014 Thanos may not have encountered Carol directly, but Ronan and his forces definitely did encounter her, over a decade earlier, and she cut through his ships like a hot knife through butter. Tales of her are bound to have spread through their forces, so she would definitely be a known threat they would want to prioritise. – delinear May 24 '19 at 8:15
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    @TheLethalCarrot - I disagree. The answer to the first question is "John Smith" (or whoever). A competent answer to that won't necessarily answer this question – Valorum May 24 '19 at 10:35
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    @nebogipfel 2018 Thanos knew who Tony Stark was because of their fairly direct conflict - in 2012 Tony nuked his Chitauri army. – MartianInvader May 24 '19 at 21:20
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Carol entered the atmosphere flying incredibly fast and full of energy going straight for Sanctuary II. It doesn't matter if they knew what/who was coming at them they merely followed the best course of action to try and protect themselves. They essentially have two options and it doesn't matter if it was a person, a spaceship or a missile:

  1. Shoot it down: blow it up before it gets near and destroy the threat and then you can continue "raining fire" but if you don't defend yourself you won't get the chance at all. Better to temporarily stop, deal with the threat and then continue.

  2. Perform evasive maneuvers: the ship is quite large so I doubt it would have been able to evade what was coming at them but it is an option. Whilst doing this the cannons would likely have stopped anyway as they wouldn't have had a clear shot at the ground.

And these options aren't mutually exclusive, Sanctuary II could have mixed both and might have done, had it survived the first assault.

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