The major theme throughout of Do Not Go Gentle and Hope Springs Eternal. Even as Unicron rips apart planet after planet and things start to look bleak, people refuse to give up hope.
How even longterm enemies come together to face this threat and all try save the universe.
The showcasing of how Rousseau Was Right. While there are of course outliers like Shockwave, for the most part people are setting aside their differences and doing their best to do good.
Moments of Putting the Band Back Together, such as the broken up members of M.A.S.K all reuniting amidst the chaos to help as many people as they can.
Arcee and Aileron throughout have many moments like this as an Official Couple.
Unicron 0:
The fact that despite their being a history of some animosity between them, the Cybertronians immediately go to help the Elonians when they come under attack, being determined to save as many as they can.
Bumblebee taking the time to comfort a frightened Elonian child as she huddles alone crying with her pet.
Bumblebee: Hey there. I know you don't speak my language but I hope you understand, your friendly neighbourhood rescue bots are here to save the day.
Bumblebee: Don't worry, I wouldn't dream of leaving your friend behind.
Despite it ultimately resulting in tragedy, the titan Emissary trying to protect the Elonians by blocking a spacebridge. Especially considering the usual attitude towards organics by cybertronians from his era.
The fact that at least 2/3 of the Elonian population, animals included, were successfully saved by being bridged to Cybertron.
Including the little girl and her pet. Bumblebee kept his promise.
Unicron 4:
Despite his declaration that the latest conflict has nothing to do with him, the moment Blurr looks outside the window of his bar and sees Unicron tearing Cybertron apart, he decides to do what he does best - run really fast and save as many lives as he can.
Cosmos, Laserbeak, Buzz Saw, and Sky-Byte joining forces to Hold the Line against Unicron's Maximals so the Decepticons of Sanctuary Station can escape safely. It may be a Bolivian Army Ending for them, but Cosmos dies among friends.
Unicron 5:
Autobots, Decepticons, G.I. Joes, Cobra forces, and all the rest coming together for one last briefing before the final battle. Some tensions aside, they agree to set it all aside, at least until the apocalypse is averted.
As night falls before the final offensive, Arcee visits Optimus, and the two share private concerns and offer comfort to one another.
Unicron 6:
As the remaining Seekers carry Optimus, Arcee, and the Talisman to Unicron, Thundercracker gets shot down and spirals out of control. As the Chaos-Bringer's minions close in to finish him off, Skywarp (having been sent to retrieve the Talisman) jumps in to take a blow meant for him.
Cue Thundercracker tossing the Talisman to Optimus, Arcee, and Starscream so he can stay behind to protect Skywarp from the incoming Maximal horde.
Skywarp: Get the Talisman out of here!
Thundercracker: But...but we're Seekers. And Seekers never leave each other behind. Starscream - catch! I've got a brother to save!
Now without Skywarp or Thundercracker, Optimus, Arcee, and Starscream don't have a way to get the Talisman inside Unicron. That is, Starscream reveals, without switching the Talisman on and using its power to bore a way to Unicron's core. Which, as he deduced, means that whoever activates it would be killed by the Talisman's unleashed energies. So does he demand that Arcee or Optimus sacrifice themselves for him? Believe it or not...no.
Starscream:...I always knew this would come down to me. Tell Windblade to take good care of Earth, will you? (Pauses, and adds wryly) Aw, who am I kidding? She probably won't even TRY to conquer the place.
Ironhide is fatally wounded by one of Unicron's attacking Maximals, but goes out with a smile because he sees how everyone - Autobots, Decepticons, and all of their respective allies - have come together to defy the apocalypse.
Jazz: Ironhide - Ratchet can pull y'back together
Ironhide: Ratchet's far away, pal...but he's also right here. I get it. I get what "Till All Are One" means. "Pax Cybertronia," too. An' it's okay, Jazz. It's really...
Despite her pessimism about what comes next should Unicron be destroyed, and an absolute lack of faith in Optimus being any better than any of Cybertron's other leaders, Slide nonetheless agrees to join forces with the remaining Torchbearers to form Victorion.
Prowl's Character Development is brought into full focus, especially compared to his Evil Counterpart, Shockwave - unlike the latter, he still believes in inherent goodness.
When Optimus is trying to speak to the dead Antilian scientist, he is assisted by the spirits of everyone who had died, including Rung, Skids, Pipes, Trailcutter, and Ravage.
Thanks to Soundwave, who sacrifices himself to ensure that the Enigma of Combination can bring them through.
When all forces start pulling back so they don't get caught in the Talisman's destruction of Unicron, Aileron and Bumblebee stay behind to rescue Arcee and Optimus. They succeed with the former.
As Unicron begins to collapse, Optimus saves the Antilian scientist from falling into the abyss alone, vowing to stay with him at the end.
The Scientist: So long ago...I can't remember. But I know the name of my daughter, who your kind murdered...
Orion Pax: Then that shall be the word. Rather than the fire of hatred...let her name - her memory - light this dark hour.
(Optimus gives the Antilian scientist a Cooldown Hug as the Talisman's energies engulf them both)
As the dust settles...
Thundercracker - having been set up to die ever since he left his dog Buster with Marissa Fairborn - survives. Him and Skywarp both, the latter acknowledging him as a proper Seeker.
Aileron and Arcee share a Big Damn Kiss on Earth's moon.
Rom and the other Solstar Knights comfort the Elonian child from the beginning of the series.
Windblade resolves that while Earth is the new home of the Cybertronians, they'll be sharing it on equal terms with the human race.
Pyra Magna comes to terms with her crisis of faith, concluding to find her own path to believe in...and teaching that same sense of self-belief to others, reclaiming the hammer that the Mistress of the Flame left to her.
Slide accepts Pyra's offer to become part of the new Torchbearers, and concluding that Optimus was never the tyrant that she thought he was.
Pyra Magna's final monologue closes out the miniseries, putting an optimistic note on the Grand Finale:
Pyra Magna: A yellow star and a miniature black hole look upon us, in equilibrium. We are touched by light and dark - judged by both. Optimus Prime is gone...and with him ends the era of Autobot and Decepticon, Cybertronian and colonist, human and machine. What survives is his faith. Perhaps he never believed in any higher power guiding out hands...but he believed inus. I am Pyra Magna, the Mistress of Flame. Spiritual leader of my people, defender of my homeworld...Earth. And we will light our way against all of our darkest hours...as one.
