Actually, I recently sat down and tried to figure out the best ordering of the 2008 serials when I was making my 2008 timeline on thegreatarchives.com. The serials are messy, but it helps if you use the release dates of the serials as a baseline and rearrange things from there (new chapters were released in a cycle for Destiny War, Dwellers in Darkness, and Brothers in Arms, in that order). Here are my notes if you want them:
The Visorak Take Over Tobduk's Island
? BiA 6: A Makuta comes to Tobduk's island and develops the Visorak. The Visorak wipe out the village. The island is renamed Visorak. Tobduk and others escape to Nynrah and then Stelt.
Vultraz Kills Mazeka's Mentor
? BiA 1: Vultraz and Mazeka live in the same village on the Tren Krom Peninsula under Gorast's rule. Vultraz leaves and becomes a villain.
A few years before Vultraz and Mazeka fight BiA 1: Vultraz kills Mazeka's mentor. Mazeka is inspired to become a hero and starts clashing with Vultraz.
5 Years Ago: Mazeka Defeats Vultraz
Five years ago BiA 1: On the Tren Krom peninsula, Vultraz wipes out a village of Matoran to get a rare lava-gem. Mazeka fights Vultraz and knocks him off a cliff, seemingly to his death. Gorast in disguise helps Mazeka climb to safety. Mazeka returns to his village to submit himself to justice.
Five years ago BiA 2.1: Gorast saves Vultraz and modifies his armor. She tasks him with finding Krakua.
BiA 2.2: Jerbraz recruits Mazeka to work for the Order and tasks him with protecting Krakua.
Five years ago BiA 3-4.1: Mazeka and Jerbraz go to the De-Matoran village to get Krakua. Vultraz attacks the village. Krakua gets away with Jerbraz. Vultraz bests Mazeka but spares him. Mazeka asks Jerbraz for training.
Federation of Fear
FoF 1: Brutaka greets his team members in a cell on Daxia.
= FoF 2: Brutaka's team sails to Stelt.
FoF 2: Brutaka's team steals a boat from the Steltian trader.
= FoF 3: Brutaka's team is at sea for 3 days.
FoF 3: Spiriah takes over the ship with his Zyglak allies.
= FoF 4: Spiriah is in control of the ship for 3 days.
FoF 4: The ship reaches Zakaz. Ehlek's species destroys the Zyglak fleet. Brutaka takes over the ship again. Lariska joins the crew.
? FoF 5: Icarax kills Botar. Trinuma stashes the weapons on Tren Krom's island and returns to Daxia.
FoF 5-6: Brutaka's team comes to Tren Krom's island. Tren Krom kills Carapar and releases the rest.
FoF 7: Brutaka's team arrives on Artidax. Takadox traps the others in a cave and makes his escape.
FoF 8-9: The team makes its way to the chamber where Miserix is imprisoned.
FoF 10: Miserix absorbs and kills Spiriah. The team frees Miserix. They fly on Miserix's back to the north.
Axonn Returns to Daxia; Ancient Recruits the Shadowed One
DW 1.1: Botar's replacement and Krakua go to Voya Nui to bring Axonn to Daxia. Axonn meets Brutaka and Miserix on Daxia.
Concurrently with DW 1.1 DW 1.2: On Odina, Ancient gets a secret signal to recruit the Shadowed One to the Order's cause.
Concurrently with DW 1.1-1.2 DW 1.3: Trinuma releases Vezon to go on a mission. All six Piraka and Karzahni are being held prisoner on Daxia.
? DiD 2: Helryx tells the Shadowed One to occupy Xia.
The Dark Hunters Take Xia
DiD 1: The Toa Hagah subdue the Tahtorak and Kanohi Dragon on Xia. The Dark Hunter fleet comes to Xia.
DiD 2: Helryx comes to Xia with Botar's replacement and the four-armed warrior. Helryx stops the Shadowed One from destroying Xia. Helryx sends the Toa Hagah to Metru Nui with Zaktan.
DW 3.2: Botar's replacement takes the Toa Hagah to Metru Nui. They tell the Toa Mahri that they have come to destroy the Coliseum.
= DiD 3: The Toa Mahri and Toa Hagah fight, then become allies.
? = DW 5.1: The Dark Hunters take over Xia in a matter of hours.
Axonn and Brutaka Go to Zakaz
DW 2.1: Axonn and Brutaka go to Zakaz and "surrender" themselves to the Skakdi under Nektann's command.
Concurrently with DW 2.1 DW 2.2: Miserix harasses the Steltian trader and says he is looking for Teridax.
Concurrently with DW 2.1-2.2 DW 2.3: Trinuma and Vezon sail toward Destral.
DW 3.1: Axonn and Brutaka convince Nektann to fight the Brotherhood.
Vezon Arrives on Destral
? DW 3.3: Trinuma drops Vezon off on Destral. Vezon is promptly captured by Rahkshi.
DW 3.3: Tridax interrogates Vezon. Vezon claims that the Destral's teleportation mechanism has been sabotaged.
Almost a Day Passes
= DiD 3: The Toa Mahri and Toa Hagah spend hours planning how to get beneath the Coliseum.
= DiD 3: The Toa Mahri and Toa Hagah spend more time convincing the Turaga to agree to their plan.
= DiD 3: The Toa Mahri and Toa Hagah spend half a day preparing for their plan to get beneath the Coliseum.
The War Does Not Begin Well for the Order
? DW 7: Helryx convinces Keetongu to help the Order fight the Brotherhood. In return, she promises to eliminate the Visorak.
? DW 4.1: The Brotherhood uses the Makuta pool island as a staging area for an invasion of the mainland. Rahkshi wipe out the island's Matoran population.
= DW 4.2: The war against the Brotherhood has not begun well. The Order controls Xia via the Dark Hunters, but they have been unable to beat the Brotherhood on Nynrah. In other places, the Order's surprise attacks meet with unexpectedly strong resistance from Rahkshi and Exo-Toa.
? DW 4.2: Given the state of the war, Helryx makes two difficult decisions. First, she sends Johmak to Metru Nui with the Heart of the Visorak. The Toa Mahri will be tasked with taking it to Artidax to wipe out the Visorak. Second, she sends a messenger to tell Hydraxon to free the Barraki from the Pit.
The Toa Hagah Go Below the Coliseum; The Order Frees the Barraki
DiD 3: The Toa lift the Coliseum, and the Toa Hagah go below.
DW 4.2: Helryx sits in the command chamber on Daxia.
DW 4.3: Hydraxon receives Helryx's orders. Hydraxon and Lesovikk free the Barraki.
DiD 4: Moments after the Toa Hagah go beneath the Coliseum, Johmak sends the Toa Mahri to Artidax. Jaller, Nuparu, and Hahli go while Hewkii and Kongu stay.
DiD 4: Within the hour, Jaller, Nuparu, and Hahli leave by ship.
DiD 4: Johmak knocks Hewkii and Kongu unconscious.
Multiple Days Pass
= DiD 4: Jaller, Nuparu, and Hahli have a long, uneventful trip to Artidax. It lasts for multiple days.
= DW 5.3 Pridak raises an army.
Icarax Summons Vultraz to Karda Nui
? After Toa Ignika beats Icarax BiA 7.1-7.2: Icarax summons Vultraz to Karda Nui via telepathy to bring him information about the place where the Makuta were created, presumably so he can heal himself.
? BiA 4.2: A rogue Nynrah ghost helps Vultraz modify his vehicle. Vultraz is planning to go to Karda Nui to bring something to Icarax.
? BiA 4.2: Vultraz raids a village on an island not far from Stelt. BiA 7.2: This is because he has to track down the place where he hid the tablets he stole.
Mazeka Goes to Stelt
BiA 4.2: Mazeka goes to Stelt, which is in an uproar after Miserix's visit. Mazeka has his swamp strider at this point. He learns from the rogue Nynrah Ghost that Vultraz has gone to Karda Nui.
? DW 5.3 Pridak defeats Brotherhood forces on the island where Zaktan found the Plan.
? DiD 4: A short time before the Toa come to Artidax, two Order agents (including Botar's replacement?) teleport to Artidax and leave equipment to make the volcano erupt, then abruptly leave. Takadox is trapped on Artidax and watches them.
Mazeka Goes to Daxia
BiA 5: Mazeka goes to Daxia without proper clearance to ask Helryx where Karda Nui is. Many Order members are away fighting the war. Mazeka finds Tobduk instead. Mazeka agrees to help Tobduk on a mission in exchange for information.
The Toa Arrive on Artidax
DiD 4: Jaller, Nuparu, and Hahli arrive on Artidax. Takadox hypnotizes them and escapes on their boat.
DiD 6: Teridax rouses Jaller, and Jaller, Nuparu, and Hahli escape Artidax. The Visorak are obliterated. The Toa Mahri head toward Metru Nui.
DW 9: = ? Jaller, Nuparu, and Hahli take a long time to return to Metru Nui from Artidax.
The Order Attacks Destral; The Shadowed One Finds the Viruses
DW 5.1: The Shadowed One discovers the Makuta viruses on Xia.
DW 5.2: After checking Destral's teleportation mechanism, Tridax continues interrogating Vezon. The Order launches its attack on Destral. Tridax goes to teleport Destral to Metru Nui.
Concurrently with DW 5.2 DW 5.3: Pridak finds the same chamber where Zaktan once saw the Plan.
DW 6.2: Ancient walks in on the Shadowed One with the Makuta viruses. The Shadowed One kills Ancient.
DW 6.3: Vezon follows Tridax to the chamber with the Takanuva army. Tridax reveals that he has an Olmak. Mazeka and Tobduk attack Tridax.
BiA 6: Mazeka lets Vezon escape. Tobduk incinerates Tridax. Tobduk and Mazeka leave Destral as the fortress is being destroyed. Vezon doubles back to the Takanuva army.
The War Turns against the Brotherhood (Note: This should probably be before Helryx becomes unavailable in DW 7)
= The Order builds major fortifications on Metru Nui and confines the Turaga to the Coliseum.
= DW 8.2: Over a number of days, Metru Nui is fortified. The fortunes of war turn against the Brotherhood. Many Makuta-held islands fall. Destral itself falls.
= DW 4.1: Axonn and Brutaka bring the Skakdi army to the Makuta pool island. The Skakdi defeat the Rahkshi army there.
? DW 7: After a long and furious battle, the Order drives Brotherhood forces from Nynrah.
? = BiA 7: Mazeka spends time getting the location of Karda Nui from Tobduk, then getting his swamp strider from Daxia. Finally, he goes to Karda Nui.
Miserix Rescues the Toa Hagah
DiD 5: The Toa Hagah go down the tunnel. They find an inscription that mentions Bara Magna. They run into a magnetic trap.
DiD 7: Miserix saves the Toa Hagah.
The Toa Hagah and Miserix Travel for Hours
= DiD 7: The Toa Hagah and Miserix travel through the tunnel for hours.
DiD 8.1: The Makuta have suffered serious defeats but are not yet vanquished.
DiD 8.1: The Order decides to make Metru Nui the site of the final battle.
Mazeka and Vultraz Go to the Melding Universe
BiA 7.1-7.4: Mazeka arrives in the Karda Nui swamp. The Toa and Makuta are locked in battle there. Mazeka looks for Vultraz. Vultraz is on his way to Icarax when he spots Mazeka and attacks him. Mazeka and Vultraz fall through a portal that opens up between them.
BiA 7.4-8: Mazeka and Vultraz find themselves on Spherus Magna in the Melding universe, where they meet "Toa" Macku and "Matoran" Helryx. They learn about the war over energized protodermis and how the Shattering was prevented. Macku directs them to the Great Beings.
Helryx and Keetongu Discover the EP Lake Island
DW 7: After the battle on Nynrah, Keetongu accompanies Helryx. Helryx discovers the energized protodermis lake island with her mask power.
DW 7: = Helryx and Keetongu take a short journey to the EP lake island.
Voporak Steals the Vahi
= DW 8.2: In recent days, Metru Nui has been fortified. The fortunes of war have turned against the Brotherhood. Many Makuta-held islands have fallen. Destral has fallen.
DW 8.2: Voporak steals the Vahi from the Coliseum and kills the four-armed warrior.
Axonn and Brutaka Find the Makuta Pool (NOTE: This has to be moved right before DiD 7)
DW 4.1: As the Skakdi-Rahkshi battle winds down, Axonn and Brutaka find the Makuta pool and fall in.
DW 6.1: Brutaka absorbs the essence of the Makuta species. He saves Axonn and insists on going to the secret chamber beneath Metru Nui to stop Teridax.
DiD 8.2: Brutaka insists they go to the chamber beneath Metru Nui right away.
Helryx and Keeetongu Meet the Energized Protodermis Entity (NOTE: This has to be moved right before DiD 7)
DW 7: Helryx and Keetongu go to the energized protodermis lake island. The energized protodermis entity sends a wave of energized protodermis at Helryx and Keetongu.
DW 8.1: A portal opens behind Helryx and Keetongu, and they escape through it. Vezon, wearing the Destral Olmak, comes out of the portal and is hit by the energized protodermis.
DW 8.3: Kalmah, Mantax, and Ehlek go to Xia on behalf of Pridak to strike a deal with the Shadowed One regarding the Makuta viruses. The Shadowed One agrees to meet Pridak in Karzahni.
DiD 8.1: Hewkii and Kongu awaken. Johmak explains that the Order has fortified Metru Nui and leaked information to make it a target for the Brotherhood. The Brotherhood has suffered serious defeats but is not yet vanquished.
Teridax Is Found in the Control Room
DiD 7: The Toa Hagah and Miserix reach the control room. They find the two Glatorian corpses. A portal opens by them.
DiD 8.2: Helryx and Keetongu come out of the portal. Then Axonn and Brutaka come out of the portal. Teridax shatters Brutaka's mask and destroys Zaktan.
DiD 8.3: Destral is in ruins. The Order sweeps the island for survivors and loot. Vezon has already left using the Olmak. One of the dark Takanuvas emerges from his canister.
Must come before Mata Nui's awakening DiD 9: Brutaka reveals that Mata Nui is the Matoran universe, and that Teridax has taken control of it. Teridax turns Miserix into a picture on the wall, traps the Toa Hagah in an illusion, and teleports Axonn, Brutaka, and Keetongu to the southern edge of the Matoran universe. He keeps Helryx captive as someone to talk to.
Battle of Metru Nui
DW 9: Jaller, Nuparu, and Hahli return to Metru Nui in the middle of the battle. They find Vakama and make a plan to awaken the Bohrok using Krakua's power.
DW 9: Hahli finds Krakua and tells him the plan.
DW 9: Hahli leaves in order to try to wreck the Makuta fleet in the water, but before she gets started, Mata Nui is awakened.
DW 9: Mata Nui is awakened.
DW 9: A storm wrecks the Makuta ships. The Rahkshi keep coming, but the Bohrok fight against them. The Toa Nuva arrive in their battle vehicles. The Rahkshi are driven out of the city.
DW 9: Vakama and Dume announce that tomorrow will be a city-wide celebration in the Coliseum.
DW 9: Hahli worries that victory came too easily and heads to Ga-Metru.
Mazeka Returns with Light Teridax
BiA 9: = Light Teridax leads Mazeka and Vultraz on a long journey to the Great Beings' fortress.
BiA 9: The Great Beings see that Vultraz is filled with shadow. The Great Beings decide to keep Vultraz for study and send light Teridax home to Mazeka's universe in exchange.