Throughout the game, we're lead to believe that the main protagonist was the hero of Oblivia. All the characters kept drawing parallels between Ben/Summer and the hero. Most important of all, the Hero's Mural depicts the story of the hero in blue clothing fighting off the Steelheads of the evil ruler.
However, after beating all the past temple missions, I've come to conclude that the Past Missions were not a prequel to the events of the game, but a prequel to that legend. All the events set up the story of the legend.
The prominent legend itself lacked any mention of Arceus but had the Sky Fortress. The Past mission on the other hand only had a passing mention of the Sky Fortress when Sabios steals the Orb (which apparently absorbs the power of Pokemon), stating that it was essential to make the Sky Fortress.
After this event, Sabios is never seen in the story again. At the end of the story, the characters mention that they will take care of the aftermath of those events and will search for Sabios. However, no one seems to know where he is, nor do they mention the Sky Fortress.
The hero's identity
This is where it gets interesting. I believe that the hero of legend isn't the Protagonist, but Ravio himself. At the end of the missions, all the people of Oblivia's past, inspired by Ben/Summer and vows to take matters into their own hands. They state the past is their responsibility and will work towards a peaceful future of Oblivia as they send the Protagonist home. They ask to not be told the results of their efforts, as Ben/Summer are from the future, so that they can properly work towards their bright future. In the end, Ravio too makes a startling vow. He vows to protect Oblivia from any future dangers. He says that he will one day communicate with Pokemon, even Legendary Pokemon, something which the Protagonist has not done through any of his ventures in the Past Missions (Arceus being the last boss means that it doesn't need to be befriended to go on, just calmed).
Tanvir claims that Ravio has gone through a lot of development and grew up now that he had someone to look up to. It would not be surprising that Ravio, who's family clothing seems to favour the colour blue (as evident by Ellios' clothes when the Golden Armor falls off) would also wear blue clothing not only because it seems to be his family colours but in commemoration of the ranger who had saved his father.
Furthermore, you see in the Hero's Mural, the hero commanding both Eon Pokemon, something the Protagonist never does. The future quest with Ravio's ghost also has Ravio testing your powers, in which he summons the last of the Eon duo to battle you. Yeah, Ravio appeared as a child here rather than the older-looking hero in the mural, but let's remember he's a ghost. Perhaps he appears to Ben/Summer in the guise of his younger self because that is the form in which you would recognize him. The mural itself also depicts a distinctly male hero rather than being ambiguous, which leads me to believe that the Hero is Ravio rather than Ben or Summer.
Now what I believe as the most important part (other than the fact that you did not befriend any of those legendary Pokemon in the past) is the lack of any mention of a "strange device" used to befriend Pokemon from the hero of legend. In the past, Tanvir has commented on your strange attire, surely a strange device such as this would have made it into legend. After all, when one writes a story, they usually try to emphasize unique features of the hero. It's not as if they would think the hero using an item would diminish his status, as they had no problem showing the hero using the Rainbow Grail to stop the Sky Fortress.
It should also be noted that after defeating Arceus, Celebi willingly keeps the portal on the Stone of Time open to allow you to revisit. Yeah, this may be a case of gameplay-and-story segregation, but I they took the time to reference this in the plot before you leave. This opens up the possibility that it is in fact the Protagonist who saves the day, and we do see them return to Oblivia at the end of the main-story. Considering that Ukelele Pichu's home is the islands, I see a lot of foreseeable visits in the Protagonist's future.
However, I find it unlikely that Ben/Summer would return to the past, or that they would be able to. Sabios is well aware that the ranger is a time-traveler, and he would likely take the necessary precautions to prevent his intervention. Other legends recited in the present mention how the evil ruler wore golden armor, so it is likely that Sabios gets his hands on Ellios' suit. Now Sabios has the most powerful armor created for controlling Pokemon, as well as an orb which absorbs Pokemon's powers. I believe it was the combination of these two items that subdued Arceus and allowed Ellios to control it, after all, Arceus only goes wild and attacks after this power-absorbing orb is removed. I'm sure no one is going to argue that Arceus is more powerful than Celebi, and if it could be controlled by the combination of Orb and Armor, then I am sure Celebi could as well.
The Ranger's role in the greater scheme of things
As I'll discuss in a later theory, I believe that Celebi plays an active role in shaping history.
Celebi, being able to time travel and likely perceiving time differently than other creatures could see the dark future which was about to unfold and brought Ben/Summer back to the past. However, the ranger was not brought back to stop Sabios but to inspire the future hero to work towards befriending Pokemon(note: things I discuss in the previous blog as well as this point will be relevant to the next theory).
When Ben/Summer arrived, Ravio was depressed that his father was always away at the temple, and the events of the Past Temple Missions began to unfold. As the missions went on, Ravio becomes disheartened to find out that his father may be behind all these events, and the people around him really aren't helping the situation. Sure Tanvir and Kira act like surrogate parents, but the two generally feel powerless to help. Not only that, but they are incredibly overprotecting and would not allow Ravio to help uncover the truth (and with good reason, he is very young and is the son of the region's ruler). However, as the ranger progresses through the temples, Ravio's (and everyone's) spirits are lifted, everyone starts to help as best as they can, and Ravio even goes so far as to investigate Teakwood forest himself.
And, as I had mentioned earlier, by the end of the adventure, Ravio vows to be like Ben/Summer and communicate his feelings of friendship to all Pokemon, even legendaries.
As for the lack of mention of Ben/Summer, I believe that Ben/Summer were celebrated heroes of Oblivia's past, but as the new evil loomed over and the lack of appearance of the old hero, praise for them fell amongst those not aware of the conditions as to why he could not appear. Likewise, the past depicted by the Oblivia ruins seemed like a dark and desolate place after Sabios completes his Sky Fortress and takes over. It would not be unreasonable to assume that any murals dedicated to the hero before his rule would have been wiped out. After all, there seems to be no mention of Oblivia's history before the evil ruler.
Going back to the topic of the Ranger's lack of appearance, I had suggested that Sabios may be in control of Celebi. This would make it unlikely that Celebi would even bring the ranger back. Likewise, even if the ranger was brought back previous to the attack, the newly controlled Celebi would likely send the ranger back to the future.
With all the Steelhead under his control, and the only person who could break Pokemon and Steelhead out of his mind control out of the way, its likely that Sabios didn't see Ravio as a threat. Even if he realized that he may be a threat, Ravio is also the closest person to Celebi and I doubt he'd risk having his control over Celebi weaken even for just a second allowing it to bring the ranger back and then escaping.
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