Well, here are a couple of loose plot threads that have yet to be tied up;
-Takanuva’s Destiny, involving his role in a Great Beings’ War that Velika intends to start
-Marendar, a Toa-killing machine now on the loose
-The Shadowed One is leading the Dark Hunters and other remnants and is armed with Kojol’s viruses
-The Barraki are now amphibious, back in their original forms, AND have their armies. Although Takadox is on his own and on the run, Pridak has basically achieved the goal he had at the end of 07.
-Atakus, Kabrua, and Perditus are agents of Velika
-Velika is trying to blow up a fortress with the Cursed Being, Helryx, and others inside; Likewise, Tuyet has the Nui Stone
-Lewa is cornered by a bunch of Agori Luddites
-Kopaka and Pohatu are on the Red Star with Mavrah, and are about to participate in a ‘Red Star Zombie story’; Likewise, we don’t know why it was broken, and Gaardus is on the loose
-Chiara, Zaria, Orde, and Gelu are being hunted down by Kabrua, who has a device designed to disable Toa powers. Likewise, Orde knows at least some parts of Velika’s plans
-The Toa Mahri have yet to reunite with Gaaki and abandon the Skakdi
-The Golden Skinned Being is roaming and about
-Metus, Ahkmou, and Tuma are out there somewhere
-Krakua is meant to be the lone hero of a besieged island fortress
-Part of Velika’s plan is to kill all of the powerful beings who can oppose him
-Alternate Teridax and Mazeka are up and about
-Several Dark Hunters have unresolved plot threads (such as Mimic finding his friend, the secrets in Minion’s mind, Tyrant’s return, Vengeance’s revenge on Mata Nui -since he killed Teridax-, Seeker retrieving the Avohkii, Amphibax hasn’t reunited with Ehlek, Conjurer is still in his coma, we don’t know where Devastator and Ravager came from, etc.)
-Voporak has his hands on the VAHI, Mask of Time
-Lesovikk is suspected or murdering Karzahni, and though we know the truth it hasn’t been spread yet
-There are still a few Shadow Takanuva mucking about
-The Ignika is being safe-guarded somewhere, and on a lesser note Umbra plans to continue guarding it as always
-The GSR is being dismantled to make new homes, and various beings are migrating out onto Spherus Magna
-The Sisters of the Skrall likely know the truth of Annona and are a loose thread
-Baterra are still hanging around, but now that Tuma and Metus know the truth, it’s likely one of them will mention it in order to save themselves and use it as a bargaining chip
-There are still Wild Rahkshi and Visorak
-Dekar may or may not have realized the truth of his origins and come to terms with it, and is going to become a Bounty Hunter
-The Pit and its prisoners are being moved out, with Maxilos and Glatorian to guard it
-The Element Lords are on the loose, alongside other villains and criminals such as Fero, Stronius, Branar, Malum, etc.
-The Bohrok may or may not be reprogrammed to help the Spherus Magna society
-The Earth Tribe is still plotting, and plan to cause disorder in the new society to save their hides
There are probably some others I missed out on, so let me see if I can figure them out.