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In episodes 9 and 10 of season six, we see Daenerys ride her dragons and destroy/capture the enemy fleet. Then she sails off with her armada, with the dragons flying overhead.

If I remember correctly though, Dany's relationship with her dragons was pretty sour last time they were together. Drogon flew off and was rarely seen. The other two had to be locked underground and chained up. Most of the time the dragons, Drogon especially, seemed pretty unresponsive to her. And yet in episode 9 they all followed her without hesitation. (Also, Drogon seems to show up at the most convenient times.)

So, how did Dany gain full command of her dragons so quickly?

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    as we would over at SFF... because magic – Skooba Jun 28 '16 at 0:53
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    @Skooba We rarely say that about ASOIAF there :P Harry Potter fans do but ASOIAF ones don't. (I have done it only one time myself) – Aegon Aug 19 '17 at 11:00
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The show simply doesn't answer this, but I think we can come up with an answer by observing the dragons' behaviour and comparing it to other animals which we understand better.

The short answer is that they are intelligent and loyal creatures.

Let's jot down a few things that we know about dragons:

  • They are intelligent (Tyrion claims that they are more intelligent than some humans)
  • They can understand language
    • At least simple commands but;
    • Possibly more complex language such as a strategy or plan (such as when they destroy only some of the Masters' ships)
  • They are loyal to their master/rider (they always respond to Daenarys and history tells us that dragons in the past were loyal to their Targaryen masters/riders)
  • There is no reason to think that they are spiteful or hold grudges for punishments
  • They cannot be truly tamed (according to Jorah Mormont) but they are clearly tamable at least to a large degree

Now compare dragons to something like dogs. If you punish a dog, even going so far as to lock it up for a time, when it comes out it still loves its master. They aren't vengeful. More than just a master or rider, Daenarys describes herself as the mother of dragons. You always love your mother (this is even true in many animals).

Drogon especially, seemed pretty unresponsive to her

The dragons were young (like puppies). I think this might explain their unresponsiveness and bad behaviour. Towards seasons 5 and 6 we see the dragons are much more mature and less playful (think back to when they fight each other over food - like young animals might).

Drogon seems to show up at the most convenient times

There isn't much in-universe explanation for this except that, as you say, it's convenient. The out-of-universe explanation would be that it has significant dramatic effect.

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    Getting into book territory, there are some mentions of dragon riders and especially wargs having a type of psychic connection with their animals. Which could explain how Drogon magically comes flying in to save Dany at the last second in season 5 and how Dany seems to know that Drogon is nearby when she's riding back to Meereen with the Dothraki. – Virusbomb Jun 28 '16 at 14:23
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It is strongly implied that the Dragon Lords are natural wargs, much like the Starks with their blood of the First Men.

Rowan's answer is valid, but the primary reason is the psychic connection.

This can be borne out by her ability to command without speech at the end of S6 when she burns the ships.

In the books & show, it is strongly implied that she unwittingly calls Drogon psychically through emotional distress in the scene at the fighting pits.

In the books, she seems to similarly call him psychically when she is stranded on the hill of bones in the sea of grass.

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I've also wondered how Daenerys finally gained such positive control over her dragons. Until her defeat of the Dothraki khals when she gained complete control over the Dothraki people, she obviously did not have control over her dragons, aside from their residual affection for her and her being able to make them breathe fire whenever she said "Dracarys". Now all of a sudden she seems to have perfect control over them.

The only possibility I can think of is that her second trial by fire (surviving the conflagration that killed the khals) suddenly awakened a telepathic link between Daenerys and her dragons that allows her to completely control them even from afar, as she obviously did during the final battle of the Bay of Dragons.

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