In The Legend Reborn, the weapons of the Glatorian were said to have an organic origin, to explain why the Mask of Life was able to alter them. The weapons, however, look like regular metal weapons, and so one fan's theory that Spherus Magna inhabitants had metallic bones was canonized. That most weapons would be forged from bone-metal makes a lot of sense when one realizes that shortly (relative to the thousands of years the story spans) before the Core War, the Iron Tribe, which supplied the other tribes with mined metal, was destroyed. With their world's foremost miners gone, the inhabitants would need to turn to another source of metal to arm themselves.
The Golden Armor from Journey's End is a blatant Deus ex Machina, no doubt about that, however it isn't the first time we've seen something with that power. The Golden Kanohi - introduced at the end of the Quest for the Masks arc, and used throughout the Bohrok Saga - were also capable of absorbing and combining powers into one tool.
Greg has also shown a reluctance to utilize Story Breaker Powers, such as ensuring that Matoro can't use his Elemental Powers in conjunction with the Iden, or not allowing time travel with either the Vahi or Olmak. So why allow Tahu to gain all of the Makuta powers in addition to what he already has? Because the series is about to end and there won't be a story to break!
The title of the series itself. "BIONICLE" means "biological chronicle". The vast majority of the characters and creatures throughout the series' run had all lived inside what appears to be a giant robot with a whole world inside it. The story is a chronicle of this robot's biology.
With Metru Nui turning out to being the Great Spirit's brain, it clears up why the Matoran were the "heart" of it; they had to work to keep the city running in perfect condition so that Mata Nui did not fall into a coma. This also made several of the Metrus take on greater significance: Ko-Metru take in and interpret what Mata Nui learns. Onu-Metru and it's archives retains the information. Ga-Metru teachs and learns the information, ensuring it would not be forgotten soon. Po-Metru process raw material to repair and maintain the other metrus, Ta-Metru does the same for the Matoran. And Le-Metru ensures all of this is easily and quickly transported. When the Matoran left, Mata Nui lost all of these abilities and was literally comatose. When the turaga said that Mata Nui was sleeping, they meant it literally. It also explains why Mata Nui was dying; most people don't do well when their brain is comatose for well over a millenium and their brain cells have literally walked away.
It's also mentioned that Teridax used a virus to put Mata Nui to sleep—not a biological virus, but a computer virus!
The training that Turaga Lhikan puts the three Toa Metru through seems rather pointless and a poor attempt at a shout out to Mr Miyagi, but once you realize their mask powers it makes sense; Whenua's mask allows him to see in darkness so Lhikan made him wear shades and had him walk around. Nuju's mask gives him telekinesis so his task was to move heavy boulders, Nuju was a scholar not a worker so he was unused to the heavy labour. Finally Onewa's mask grants him Mind Control, which is why he was to share in his brother's tasks equally; he was suppose to manipulate them into accomplishing it for him. Lhikan, having been a veteran toa, would have recognized their masks and knew their powers long before the Toa Metru did, which would explain how he knew what tests he would need for them. Unfortunately the three Toa Metru ended up finding out about their power through their frustration with eachother instead of realizing the point of their training.
The Kanohi Masks of Power worn by nearly every major character in the Bionicle storyline function on many different levels depending on the user; for example, the Matoran villagers wear powerless Kanohi, since they lack the strength of will to use the powers of their masks. The Toa heroes wear Great Kanohi which are at full power, and the Turaga elders wear Noble Kanohi, which still retain their powers but are significantly weaker than the Great Kanohi worn by Toa. We are then left with unique masks like the Avohkii (Mask of Light), and the Kraahkan (Mask of Shadows). Then there's the Legendary Kanohi, masks so powerful that if they were damaged, their power would leak out and cause untold destruction to the Matoran Universe. The only three Legendary Kanohi we know of (so far) are the Vahi (Mask of Time), the Ignika (Mask of Life), and the unnamed Mask of Creation worn by Artahka. TIME, LIFE, AND CREATION are the most important things in the Matoran Universe. The Ignika (and possibly the Vahi and Mask of Creation) is shown to be capable of independent thought; unlike the 'normal' Kanohi, they can literally choose who can use them, which is particularly useful if any of them fall into the wrong hands.
In Mata Nui Online Game, during the Battle for Kini-Nui, cutscenes depict the Toa Kaita's journey through the Mangaia. Once Akamai and Wairuha part ways, the cutscenes focus exclusively on Wairuha, and Akamai does not appear again until he returns in a Big Damn Heroes moment to save Wairuha from the Manas. Why is this so? Because the cutscenes are visions experienced by Takua due to his mental link with Gali, who is one of the three Toa forming Wairuha. Had Tahu, Onua, or Pohatu formed that mental link instead, the cutscenes would have focused on Akamai instead of Wairuha.
Masks are central to the story, especially in the early years. In 2009 it was revealed that the island of Mata Nui was a camouflage mechanism to hide the Great Spirit Robot's face. The entire island is a giant mask.
The Toa Inika all had the same Kanohi masks as the Toa Mata when they were Matoran-which could count as a kind of subtle Foreshadowing that they're meant to be Toa. Similarly, Matoro's role as The Chosen One is foreshadowed in the Inika commercial, where he's seen standing at the front and center of the team instead of Jaller.
All of Teridax's primary defeats (his fight with Vakama, Takanuva, and Mata Nui) all involve him being crushed by a massive stone (a huge stone pillar, the Mangaia Door, and a piece of Aqua Magna). At first this might seem like an odd coincidence... but note the punishment of Pride in Dante's Purgatory; being forced to carry large boulders in order to learn humility, unable to stand with their heads held high. Given Teridax's fatal flaw, these three defeats suddenly become far more symbolic- most especially when he lifts the door to Mangaia, where's visibly struggling and kneeling underneath the weight to help others as Takutanuva.
Speaking of Teridax's defeats: throughout the story, he lost every fight he had with good guys, he won every fight against bad guys, and when he battled a Lawful Neutral Hydraxon or morally ambigious Brutaka, it ended with a tie!
In The Kingdom universe it's said that even the Island of Mata Nui will soon not be habitable either. This makes sense since later on in the main universe it's revealed that the island is being propped up by Mata Nui's face. If the Great Spirit has died this means that whatever kept his body afloat in Aqua Magna is now offline, and he is slowly sinking into the ocean floor.
The announcement that the Mask of Creation is on the same level as the Masks of Life and Time was greeted with some skepticism. But the Matoran are all about creation; if they don't do their jobs, as seen in the case of the Great Disruption, then Mata Nui will start dying. For them to lose their creativity, as would happen if the Mask of Creation was smashed, it would be just as bad in the long run as if one of the other two was destroyed.
The only three surviving Makuta in "Dark Mirror" were Teridax, Krika and Kojol. It makes perfect sense: all three relied on strategies that required patience, secrecy and waiting (Kojol knew the location of Artakha and never told anyone, making him an important asset for Teridax) in canon. Of course they would run away and hide while Gorast, Icarax and Antroz were being smashed by Toa Empire.
Icarax' love for melee combat? His mask only absorbs life energy from intact bodies, which do not usually remain after plasma blasts and acid-based attacks. He took the Kraahkan on Teridax's orders, but decided to wear it himself out of his pride and ego, as he believes that he would make a much better leader for the Brotherhood than Teridax. Because of this, it isn't too surprising that his name is two letters away from being Icarus, a figure in Classical Mythology who let his pride get the better of him, which led to his death.
Velika being a disguised Great Being actually makes a lot of sense in hindsight - during the Voya Nui novels, Velika is shown to know things that no random Po-Matoran, no matter how intelligent, should be able to know, but the other characters, and by extension, the audience, wrote it off. For instance, in Power Play, it's never explained how Velika knew that Energized Protodermis would counteract the effects of the Piraka's Antidermis Virus. In fact, he shouldn't even know what Antidermis is; not even Zaktan knew what it really was. Velika, however, was one of the beings who created Antidermis and experimented extensively with its counterpart. Of course he recognized it for what it was and knew exactly how to counteract it!
The Piraka losing to the Toa Inika actually makes a kind of sense. It's implied in Power Play that Hakann was staying out of the fight until he got cornered by Jaller, meaning that he wasn't going to use his mental blasts which proved so effective against the Nuva. Furthermore, while the Inika were new to their powers, it's worth bearing in mind that they're not newbies. All of them had spent the last millennium and a bit fighting Rahi on Mata Nui. Hewkii, Jaller, and Kongu in particular were the leaders of their respective koro's defense forces. Furthermore, their masks being organic meant that they got to avert a lot of How Do I Shot Web?. Thanks the Matoran, the Inika knew more about the Piraka and their abilities than the Piraka did about them. On top of that, the Piraka were probably overconfident from having beaten the Nuva (which happened in large part thanks to Plot Armor and Hakann having his mental blasts).
Moreover, why did the Red Star give the Inika those weird organic masks? Because of the urgency of their mission, they couldn't afford to spend time trying to figure out what their masks did or how to activate them like most newbie Toa do.
It's also not that surprising, on reflection, that they got organic masks on a quest to find the Mask of Life.
Though Takanuva's revival at the end of Mask of Light is a bit of an Ass Pull, Jaller's revival makes a lot more sense after the reveal that deceased beings go to the Red Star to be repaired, but are unable to come back because of the Red Star's broken teleportation function. Jaller's body was not destroyed, but he seems to suddenly disappear after his death, with only his mask left behind. Takutanuva was able to revive Jaller by using Makuta's teleportation power to bring Jaller back from the Star.
The fact that the Toa Mata were each given a Kanohi Miru - Mask Of Levitation - seems odd when the Kanohi Kadin - Mask of Flight - would seemingly render it redundant. However, throughout the Voya Nui saga, the Kadin is shown to have a steep learning curve that takes Nuparu most of Power Play to get the hang of (and that's with a sentient mask, to boot), while the Miru is relatively easy to use. The Toa Mata were given their identical sets of masks by Artahka for the quest to awaken Mata Nui, a mission that theoretically shouldn't have a lot of time for practice. It makes sense that he'd give them simple, but reliable and easy to use Kanohi, compared to some of the flashier but harder to use or more situational Kanohi that other Toa teams use. In fact, all six of the original Kanohi - force-fields, Super-Strength, Super-Speed, water breathing, x-ray vision, and levitation - can be seen as Boring, but Practical; easy to use and covering most obstacles the Toa Mata could reasonably be expected to encounter on the journey to Karda Nui.
There's also the fact that we later discover the Toa Mata had had some training and experience before they ever entered their canisters: Enough that they could learn how to use their masks and powers, enough so that, should they ever be needed, they wouldn't have to start out as total newbies. It was only due to the canisters malfunctioning that they lost all their memories. And even then, some hints remained in their subconscious. Even during the 2001 story arc, they didn't seem to have as much trouble with their masks and powers as the Metru and Inika did—because they'd already gone through those early days and had already mastered their abilities, they just didn't consciously remember it.
It seems a little odd that the Order never realized Hydraxon was dead, despite not having heard from him for 1,000 years. However, it's also worth bearing in mind that, as jailer of the Pit, he most likely didn't exactly file regular reports anyway. Presumably they wouldn't have heard from him regardless save for some emergency—he could've summoned Botar or swam up to Voya Nui to talk to Axonn and Brutaka if he needed to, but otherwise would've kept himself to himself.
Also, given the incredibly long lifespans of many of the characters—Helryx and Axonn, for example, are over 100,000 years old—not hearing from someone for a millennium is the human equivalent of, say, a few years at most.
Not a single important character of Chronicles period has 's' in their names. None of Toa Mata or their Kaitas, future Toa Inika, former Toa Metru, the Chronicler's company, Rahkshi, Bohrok, Bahrag, Rahi Nui and even Makuta have 's' in their name. Only in the latter half of 2003 we're introduced to several unimportant NPC Matoran who break the pattern, and in 2004 it's finally broken by Vhisola.
In The Mask of Light arc, Takua and Jaller constantly argue over Jaller being claimed as the Herald of the Toa of Light, the person destined to find the Toa of Light and deliver the Mask to him. Jaller was called the herald because the Mask shined its light on him, but both Jaller and Takua believe Takua is the real herald because he was the one to find the Mask, and (as sharp-eyed viewers will see), the Mask glows whenever Takua touches it. However, by the end of the arc, it’s revealed that Takua IS the Toa of Light. Which also makes Jaller the REAL Herald, as he was the one to carry the Mask, but also the one who “found” the Toa of Light by recognizing that Takua is the Toa and helping him realize it with his sacrifice. And, of course, he fulfills the prophecy of delivering the Mask to Takua on his deathbed, when Takua is finally ready to accept the mantle of Toa.
The Death Chamber the Toa Inika face on the way to the Ignika actually makes perfect sense. The voice warns them that one person must die as a trade for the power of the Mask of Life—which, as we later discover, is exactly what must happen in order to wield it! By having one person summon up the courage to lay down their life in order to get the mask, it all but guarantees that the potential wielder will be ready, willing, and able to do so again when they actually need to use it, and won't have to waste time in an emergency situation like Mata Nui dying with long goodbyes or building up their nerve.
It also serves to ensure that only a Toa or someone similar could access the Mask—someone wishing to steal the Mask and use its power for selfish purposes would, by definition, never be willing to sacrifice their life to do so.
Alternate Universes are by default seen as less important that the main one, simply because in the BIONICLE fiction, they are merely side-branches of the main timeline. This means that no matter what atrocities may happen in those worlds, these are simply glossed over. For example, just think of Tridax: he kidnapped and forcibly corrupted a whole bunch of Takanuvas from various other dimensions, who were then either killed during the Destiny War or freed and then killed by the Alternate Teridax. Not only does this mean that the main universe characters condoned killing originally innocent Toa who only turned evil due to a crazed villain, but also that all those other universes have been robbed of what's possibly their only Toa of Light, one of their most powerful heroes. But since they aren't the main universe, they don't seem to matter.
Boxor are made of Bohrok. And what are Bohrok? Former Av-Matoran. The Matoran used the parts of their 'un'dead brothers and sisters to fight against more of their 'un'dead brothers and sisters!
The fact that the inhabitants of Spherus/Bara Magna have metallic bones which, apparently, can be reforged into weapons/armor/what have you opens up a whole can of horror. First of all, we have a group of marauding bandits called the Bone Hunters. Instead being of merely a perjorative, the name seems to be literal— meaning that not only would they go after travelers for their possessions, but also for their skeletons. Of course, this ' bone metal' would need to be reforged, which a tribe of nomadic bandits couldn't do on their own. This is where the Skrall factor in. For starters, nobody from the other tribes visited their city Roxtus even in peacetime because...nobody who visited there ever came back. It wouldn't be a big stretch to assume that any visitors were killed for their metal. In addition, they'd probably be the ones who'd buy the 'bone metal' from the Bone Hunters and reforge it to fit their own needs. (Granted, the other villages probably do this sort of thing too, but they probably don't kill off members of other villages to do it. Or they haven't had to since the Core War.) Kiina and Berix were VERY lucky Mata Nui saved them.
The revelation that the Red Star actually revives the dead brings some really horrible thoughts about the ones that died permanent deaths. It's implied that Matoro, Icarax and the many Shadow Takanuvas are not only killed off for real, but that they would be denied to what's essentially the heaven and reincarnation of the matoran universe. Worse would probably be Tuyet from the Toa Empire Universe, who got killed in-between dimensions, dooming her consciousness to float in the endless void and no one knows it!
As the story serial Yesterday Quest reveals, Orde is the first Toa of Psionics and one of the first Toa created, so he likely was a contemporary of Lesovikk and his Toa team, maybe even worked alongside them. Now recall Orde's assignment to pacify the Zyglak and his rather ignominious failure which made them much more aggressive and violent. Now, how did Lesovikk's team die again?
The Karzahni (the plant) mentioned that a member of the Order of Mata Nui told it about the organization before it died. However they died, and whatever the Karzahni did to encourage them to talk, was probably not very pleasant at all.
Why did Makuta plan to leave Lewa behind when he dumped the rest into space? He wanted a replacement for Helryx who not only wasn't responding to his attempts to psychologically torture her into submission, but was becoming a hassle not worth the effort anyway. And who could be more satisfying to break mentally than the Fun Personified Toa Lewa?
Teridax's habit of preferring to simply be referred to as "Makuta" becomes a grim piece of foreshadowing when it becomes clear that his plan involved the genocide of the entire Makuta race. From the moment he first appeared, he was planning for "Teridax" and "Makuta" to become synonyms as the last of his kind.