With the battle against the Alternative pressing on, Hydron shows up to lend a hand. Meanwhile, Professor Clay, while inside the lab on the Alternative, receives a video transmission from Neathia, just as Mira and Keith arrive to make one final appeal. Once the Brawlers realize Mira and Keith are missing, they deduce that the siblings may have found a way inside, so Dan uses JetKor to blast a hole in the Alternative, while Gus and Marucho stay behind to guard the rear. Gus and Vulcan are nearly beaten, but Hydron steps in and saves them. Shun suggests they find the power reactor of the Alternative. Shun, having memorized the blueprints of the machine, leads the Brawlers through the Alternative. However, they are all quickly caught in a trap against four mysterious Bakugan, unrecognized by Drago, because they were from Neathia and Gundalia. While Mira pleads with her father to abandon his evil plans with Zenoheld, Dan and the others destroy the four unknown Bakugan, as well as the Power Reactor. As they make their escape, Professor Clay saves Mira from falling debris but is trapped on the ship and Hydron captures his father, forcing them both to "go down with the ship." Professor Clay returns to his computer and finds that the video he received depicts Bakugan in war. Just then, the ship explodes, instantly killing Clay, Hydron, and Zenoheld.The Resistance go their separate ways as Keith and Gus thank Dan for showing them the error of their ways. A few weeks later Marucho has completely repaired Bakugan Interspace and uses Akwimos to test it while Shun uses Hawktor and Dan sticks with Drago. The season ends with Dan, Marucho, and Shun being approached by an unknown boy who asks them if they are the Bakugan Battle Brawlers.
- The Resistance continues their battle with the Alternative.
- Hydron returns and joins the Resistance to help them against Zenoheld.
- Mira and Keith confront Professor Clay.
- Shun reveals that he has memorized the Alternative's blueprints and that its crippling weakness is the main reactor.
- Dan equips JetKor to Drago, who then blasts a hole in the Alternative.
- Dan, Shun, Ace, and Baron head to the reactor core, so Marucho stays at the entrance to guard the rear while Gus and Hydron continue fighting the army of Fortresses outside.
- Dan, Shun, Baron, and Ace encounter four unfamiliar Bakugan that Clay cloned from the phantom data: Pyrus Snapzoid, Subterra Clawsaurus, Ventus Farakspin, and Haos Lumitroid.
- Dan, Shun, Baron, and Ace destroy the four Bakugan and then blow up the reactor core.
- Dan, Marucho, Shun, Gus, Baron, and Ace all evacuate the Alternative.
- Hydron has Dryoid impale Farbros in the neck, destroying him, and then kidnaps Zenoheld, planning to make the "captain go down with the ship".
- Mira and Keith attempt to evacuate with Clay, but he chooses to stay behind.
- Professor Clay finds a video transmission that shows two factions of Bakugan at war.
- The Alternative explodes with Hydron, Clay, and Zenoheld still inside, killing them all instantly.
- Keith, Gus, Mira, Baron, and Ace all return to Vestal.
- Dan, Marucho, and Shun all return to Earth.
- Marucho spends several weeks repairing Bakugan Interspace.
- Preyas, Elfin, and Ingram all return to New Vestroia sometime before Interspace is repaired.
- Shun chooses Hawktor to be his new partner, while Marucho picks Akwimos.
- Dan, Marucho, and Shun are about to test out the rebuilt Interspace, but are interrupted by an unknown boy.
- Helix Dragonoid
- Helios MK2
- Alternative Weapon System
- Saint Nemus
- Minx Elfin
- Magma Wilda
- Rex Vulcan
- Master Ingram
- Shadow Wing
- Knight Percival
- Merlix (video footage)
- Luxtor (video footage)
- Dharak (video footage)
- Lumagrowl (video footage)
- Lythirus (video footage)
- Krakix (video footage)
- Strikeflier (video footage)
- Sabator (video footage)
Bakugan Trap Seen
Battle Gear Debuts
Battle Gear Seen
- In the Japanese ending, it's shown the events after the episode and before the epilogue. Baron is seen playing with his siblings and accidentally he hits a ball on Ace. An enraged Ace chases him with the ball. Shun and Alice are shown with Marucho as he repairs the Bakugan Interspace. Mira is seen spending time with her brother and Dan is on Earth, eating curry at Runo's restaurant as Runo and Julie look at him and Drago laughs.
- The time that Marucho takes to fix Bakugan Interspace is different in the Japanese, English and Chinese version. In the Japanese version he takes six weeks to fix Bakugan Interspace, three weeks in the English version, and one week in the Chinese version. Thus there is a time disrepency in each edition of the episode.