This is basically how I would end the unresolved Bionicle stories (Yesterday Quest and Powers that Be), and usher Spherus Magna into a fresh start. Hope you enjoy:
Gelu's team met up with Helryx's group and defeated Velika. Angonce introduced himself to them and took him and Tuyet into custody. The team then found Lewa and returned to Tahu, saying that the Great Beings wish to be left alone.
Vezon and the cursed Great Being left and haven't been seen since.
Meanwhile, Kopaka and Pohatu found Lhikan on the Red Star. He told them that the Kestora were keeping them for slave labor since they couldn't be sent home. The heroes defeated the Kestora. Rather than fly down to Spherus Magna, the residents of the Red Star decided to go out and explore space. Gaardus returned the Toa to the planet.
After everyone regrouped, Marendar made its move and killed several lesser known Toa. The Toa Nuva, along with Axxon, tried to go to the Skadi for help, as they had access to the Dreambringer. However, their new warlord told them that the Dreambringer left them, as he felt like they didn't deserve him.
Marendar then enlisted the Baterra for help in its Toa purge.
There had still been conflict between MU residents and SM residents, but Takanuva was able to bring both parties together to fight the common enemy, telling them that peace between the groups is what Mata Nui would've wanted. This is
was Takanuva's destiny.
The Toa and Glatorian went into battle: Glatorian fighting Marendar and unarmed Toa using their powers to defeat the Baterra. Marendar proved strong, but Ackar eventually destroyed it, sacrificing himself in the process.
Takanuva and the Toa Nuva then became Turaga, transferring their power into Toa stones for use in the future, should new Toa ever be needed. Takanuva used his immediately and chose Tanma to be the new Toa of Light.
Over the next few years, the Matoran and Agori built the city of New Atero,which combined Metru Nui technology with Agori architecture and customs. Other species have spread out across the planet.
After millennia of conflict and hardships, all was finally well.
But yeah, that's just my idea. Throw in your own if you've got any!