Clash and Wrath of the Titans is a trilogy arc in Season 2 of the discovery and awakening of both Trypticon and Omega Supreme.
During an exersion to find Cybertronian technology, MECH had discovered the remains of the Decepticon vessel, the Nemesis deep within the Pacific Ocean. This let out a distress beacon to both Maximal and Predacon alike. Silas, knowing full well of Aelita's capabilities as a Living Energon source, kidnapped her and brought her to the vessel.
However, the young girl had realized what the Nemesis truly was. She begged Silas not to force her to awaken the ship, telling him that the Ship itself was a Cybertronian of untold terror. This only furthered Silas to force her to awaken it, claiming that it would be grateful and indebted to MECH in awakening him. However, the Maximals and Predacons charged into battled against MECH, once again making a truce to defeat a common enemy, and also Megatron realizing the dangers if Trypticon awoke. The battle was fierce, but ultimately futile, as Silas was able to force Aelita to awaken Trypticon's spark and repair his damage, by threatening to kill Justin.
The beast had finally awakened, and transformed wtih the occupants still inside, and remained unharmed of the sequence. Silas, being as arrogant in his efforts, commanded Trypticon to expel all foreign enemies from his body. He agreed, only to expel all except Aelita, whom he kept for himself, claiming that only Megatronus was the one to command him.
Trypticon transformed into the Nemesis, and flew off, leaving all three, Maximals, Predacons, and MECH to witness, as it flew off elsewhere on the globe. Now freed, the Beast was free to unleash complete terror, and fulfill whatever mission he was sent for.
Once the Nemesis begins to run amock across the planet, the Maximals and Predacons, still working together, must find a way to bring down the Titan Decepticon. It was Grimlock, who silently wished for the Axalon to be functional. Rattrap quirked that they needed more than just a ship, they needed a ship that was die-cast constructed like Trypticon. Unfortunately, that technology was lost to Cybertron since the ending of the Great War.
However, Megatron, who was a prodigy of History, had remembered a file he had come across during his excurison of what he was looking for on Earth. It listed the location and resting place of an Autobot Ship that was still in one piece. One that in the future would be the guardian and protector of the first outpost between Cybertron and Earth's new city, the place where the now destroyed Antigo would be rebuilt on, Metroplex. The ship was located in the ruins of Antigo, underneath the town itself, in the ruins of the fabled fortress, Autobot City.
With a little help between brainiacs; Justin, Blackarachnia, Rhinox, and even Rattrap, they had accessed the city to reemerge from the ruins of Antigo, not only giving the Maximals and citizens of Antigo a new home, but also a fortress, and access to the long dormant Omega Supreme, much to Optimus's amazement.
With a little patience, and a lot of help from Maximal, Predacon, and Human alike, they had rigged an Energon power source within the Mini-Ark, and re-energized Omega Supreme, fully awakening him. Asking for his help, the mighty Autobot Guardian agreed to help in defeating the infamous Trypticon.
Preventing Trypticon from destroying New York, the two Giant Transformers duke it out in the skies. The battle was intense, nearly causing destruction of New York, until the sky battle led to Liberty Island's shores. The two robots transform, duking it out with their fists and blasters, colliding with one another constantly. During the fight, Trypticon launches his boarding coils into Omega, in an attempt to rip him apart from the inside. However, the Maximals and Predacons use this to enter Trypticon, in an attempt to rescue Aelita.
After a fierce battle against drone anti-bodies, Justin makes it to the Main Spark Chamber, in which Aelita is slowly becoming merged with Trypticon's spark. However, the defenses around it, only proved difficult to get through. He was almost about to give up, until Wind-Rider spoke through his comlink, telling him to tell her how he truly felt about her. Justin finally confesses his true feelings for her, enabling her to have the strength to fight back, pulling away from Trypticon's spark.
Trypticon, sensing this, attempted to try and pull her back, but with her newfound feelings powering her, she enabled to unlock the Omega Matrix, shutting Trypticon's spark back to its dormant state. The mighty Decepticon Titan transformed back into the Nemesis and remained in that locked state, possibly forever.
Now that Trypticon was back in stasis, the Predacons ended the truce, and now armed with the Nemesis, prepared to attack the Maximals now in Omega Supreme. However, Aelita managed to try one more trick, and set off a Transwarp teleportation, randomly sending them somewhere on the planet. Omega Supreme returned to the new Antigo, powering down and on standby, should the day come his services would be needed again. A dismayed Rattrap pouted and temper tantrumed that they finally had a working spaceship, only for him to go back to sleep.
Wind-Rider, on the other hand, and secretly heartbroken, simply stated that it wasn't a total loss. She pointed to the newly coupled Justin and Aelita, as they kissed for the Maximals to see. In which Cheetor whispered to Foxfire, "It's about time."
- Omega Supreme and Trypticon from War for Cybertron made their debut.