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Night Fury's are rare, we know that, but exactly how rare? Do we have a definite answer (if we do, please tell me I want to knoww)? At the very least, we know (assume?) that Toothless is the last of his kind... during Hiccup's life (see where I'm going?).

Based on pure speculation on my part, I think Grimmel is about Stoick's age, maybe even younger, and he's known as the "Night Fury Killer", and (I think) we don't know what age he was when he received that title. He could've been Hiccup's age in the first movie for all we know when that was bestowed upon him (I've not watched the third movie in a while, correct me if I'm wrong please).

Drago is another thought, which I estimate to be closer to Stoick's age, and it does appear he wears a cape made of dragon skin similar to Toothless's, and we know in RTTE (at the very least) just how many people want to get their hands on anything Night Fury related (including Hiccup, I believe), so I would assume that it would be difficult for Drago to aquire such a significant chuck of it.

My point is of bring the villains into this is: when Stoick was Hiccup's age/ fifteen (15), were there more Night Fury's attacking that eventually dwindled down to one (1)? We know that Cloudjumper (a Stormcutter) was present when Hiccup was an infant, but that species no longer attacked during Hiccup's older years, so it seems plausible (in my very biased opinion) that other species would also sloooowllly peter out until "the main five (5)" species remained attacking (Deadly Naddars, Hideous Zipplebacks, Monstrous Nightmares, Gronckles, and Night Fury(s?) ).

Ok, I see you're sick of speculations (that was a ramble I'm sorry :[ forgive me? No? Mk), so I'll provide very tiny in-film evidence, and a counter-argument, because that makes it funner :D

Evidence:

1). Toothless takes his time to find a place to land, initially following the flow with the rest of the dragons dropping their haul into the smog below. Why? Why not immediately fly to where he eventually lands? We see Gronckle eggs and Gronckles shying away after the dragon gets eaten by the Red Death, so that implies that dragons have at least a general place of habitation (or maybe just for laying eggs, I don't know), but Toothless eventually loops behind a piller before landing, despite knowing he may be punished for not returning earlier/ not returning with prey.

2). Toothless pretty continously glances around anxiously, left and right, like he was searching for someone (imo). And he eventually must not find then, because I don't think he really landed where he was last looking.

3). Stoick makes a comment, implying that there's been multiple Night Furys attacking at some point during his life ("Any Night Furys?"). How long may it have been since he last seen more than one? Was it before or after Hiccup was born?

4). We've seen, just before Hiccup shoots Toothless down, that it's very hard to distinguish any features about a Night Fury from afar, quite literally a shape that periodically blocks out stars (at least at night). What are the chances that it wasn't always Toothless? That they got confused with another Night Fury, maybe thinking it was the same one? They obviously didn't know what a Night Fury looked like until Toothless broke into the ring to protect Hiccup from future-Hookfang, and yet Gobber recognized what dragon this immediately was (something I've found odd, but chalked it up to the scales and overall shape).

5). Referencing to #4, was there more than one Night Fury ever attacking at once while Hiccup was a teenager, but they didn't know? We see in the fight with the Red Death above the clouds just how fast Toothless/Night Furys are (and invisible), so if Berkians knew that, did they assume that only one was attacking, just moving very quickly, when in reality there was more than one?

Counter-argument:

1). Toothless could've just been looking around at the other dragons, making sure they don't noticed/focus too strongly on the fact that he was carrying two humans, and know they might take this opportunity to steal the humans away from Toothless or sacrifice Toothless as well for bringing their enemies into their nest.

2). Hiccup only ever says "the Night Fury", while Stoick asks "Any Night Fury's?" During the first film. This could mean that Stoick grew up with Night Fury's also attacking, but by the time Hiccup was born (or at least old enough to recognize the different species by name), only one (1) remained, and Stoick was speaking out of habit due to how he grew up. Considering Toothless is the same age as Hiccup, it would make sense that Toothless once attacked Berk with his family/species until each of them were hunted down by Grimmel and he was left to be the only Night Fury to serve the queen. (I do have other thoughts of how he came to serve the Red Death, but that's not relevant here).

3). We know that no one on Berk (I didn't say from-- again, that theory is not relevant here) ever shot down/killed a Night Fury until Hiccup, or at least didn't think to record it somewhere. Astrid does mention that they've been fighting the dragons for generations going back 300-400 years, if I remember right (the numbers conflict a few times, I believe). Toothless could very well be the only Night Fury Berk has ever seen, but I feel like it doesn't completely explain Stoick's "any Night Fury's?" comment completely.

4). The rarer the species, the less likely of a chance that one of them would have a chance to be killed, and we know that Night Fury's (or at least Toothless) have a long shot range, something that the Berkians didn't have to counteract besides using catapults, and what with the boulders they need to lose, aim, and finally fire, a dragon is likely to see the large object and swerve to avoid it. One of the reasons why Hiccup was able to shoot down Toothless was because he used a small contraception with bolas (meant to capture, not kill) and sat on a dark cliff in wait, as opposed to the catapult being on its only little island and very tall, with many men yelling around it. Heck, that Monstrous Nightmare went right for it, appearing unafraid.

Interesting Extra Thoughts:

1). Toothless never stole food, yet still attacked Berk. Could he be getting revenge for something? He actively aimed for the catapult--never, if rarely, attacking elsewhere--where he knew several Berkians were. That Monstrous Nightmare knew and left in a hurry when he heard Toothless about to fire.

2). Toothless doesn't appear to be loyal to the queen (again, not stealing food for her), but still returned when the other dragons were bringing in their haul. It could be to show Hiccup what exactly was going on on their island, and why they stole food, but we saw just minutes before that how protective Toothless is of Hiccup, between leaping to go after Astrid to demanding she apologize to Hiccup (there was a different post I saw a while ago how Toothless tends to demand respect on Hiccup behalf, but I don't have it saved or remember the writer :( ), and later he jumps into the ring to protect him from future-Hookfang, knowing he was exposing his friendship with Hiccup to an entire tribe of vikings that wanted him dead, and that he couldn't fly without Hiccup's help. I find it hard to believe he would take Hiccup and his now-friend to a place he actively fears unless there was a strong reason why he would return.

Based on what I've noticed, I've come to a potential explanation of what happened:

Berkians fired a catapult, maybe aiming for a different dragon. This other Night Fury was flying behind said dragon, and didn't notice it until it was too late. Injured, they either had assistance or made it back by themselves to the nest.

The Berkians who fired the catapult didn't notice it, what with the general chaos around them, reloading, and being unable to see the Night Fury very well to begin with. The roar of pain (similar to the one Toothless let out) was drowned out around them. One of the reasons why Hiccup heard it was because he was in a much more isolated spot, away from the shouting and the light and the people.

Toothless finds that the other Night Fury was injured by the catapult, and maybe the queen demanded that the Night Fury still goes out to fight and gather. This breaks what little loyalty Toothless had to the Red Death, and refuses to bring back anything for her, but plays the part of two Night Furys well. Other dragons may/may not notice this, but since they're all stuck together, they keep quiet. They too, are tying to survive. The injured Night Fury does their best to blend in with the dark walls around them, and stays as still as possible, hoping to be ignored.

Toothless primarily aims for the catapult and the people on it, so that no dragon would ever be harmed by it again. Whether it's a few days or a few years later, Toothless gets shot down, released, befriended, and made a new tail: but someone needs to be with him. He also starts to realize that there are good humans.

Astrid shows. He does a whole bunch of crazy stuff until she apologizes, and works with Hiccup to change her mind as well. He becomes aware that he just flew into a return raid, and realizes that this is his chance to check up on the injured Night Fury. Dragons give him odd glances, wondering where he's been and why he's with people. Some are angry about this.

Toothless flies as normal, but the inhured Night Fury isn't there, and he begins to panic (I'm not sure of the exact timeline of when Toothless gets shot down to when he returns to Dragon Island with Hiccup and Astrid, but I assume anywhere from five (5) days to two (2) weeks). He eventually has to land and remains out of sight of the Red Death, until she catches a whiff of him, and they escape.

They return to the cove, and Toothless wanders away for a few minutes to grieve and get something to drink, probably feeling very guilty that the Red Death found out about the hidden Night Fury and killed/ate them and he wasn't there to stop/protect them. Maybe he feels like he abandoned them when he was supposed to be covering for them.

Toothless later rushes to the ring, because he won't abandon anyone else he cares about in their time of need. He gets captured, taken to Dragon Island--the last place he wants to be--Hiccup comes, they defeat the queen, and Toothless spends those days that Hiccup's unconscious watching over him in a way he wasn't able to with the injured Night Fury.