Ultra Magnus says this while showing Orion around the ship.
"And this is where we spend most of our time, fine-tuning strategy, reflecting on our progress to date, and debating the pedagogical constraints of logic, grammar, and rhetoric.... Has someone been drawing on the navicomp?"
Hardhead and Wheelie have this exchange while walking onto the Lost Light:
Hardhead: You remember last year, when Rodimus gave his big speech about a quest to find the Knights of Cybertron? I was this close to signing up.
Wheelie: Made-up knights impossible to find—and so you decided to stay behind.
Ultra Magnus confuses Getaway with his usage of the term "MEH".
There is apparently a conspiracy theory regarding Ultra Magnus actually being just a little guy in armor. Obviously making a reference to Minimus Ambus actually being a small 'bot wearing the Ultra Magnus armor as seen during the 'Remain in Light' arc.
There's a holographic newsboard on the Lost Light, delivering news to the crew. Amongst the announcements are things like "Xaaron’s debating society. Upcoming topics: Forged & Constructed cold", "Swerve’s. Everyone welcome*. No guns. No swords. No briefcases. *Restrictions apply", "Autobot code refresher courses. Ignorance is no excuse. 10,000 pages in only two weeks.", "Cybercrosis. The hidden killer. Free check-ups. See Ratchet. Medibay.", and reminders from Ultra Magnus to vote and wear your Autobot badge straight.
Dark Cybertron #4 (MTMTE #24)
Brainstorm's conversation with Perceptor regarding the aquatic capabilities of the Lost Light.
Brainstorm: Underwater! Lucky for us, the Lost Light was built as a submarine, eh Perceptor?
Perceptor: Is that true?
Perceptor: Really, though?
Perceptor's overly dramatic pose explaining how the Ammonites hitched a ride on the Lost Light's quantum slipstream.
And then Perceptor and Brainstorm finishing each other's sentence.
The Lost Light's crew ends up having to employ a submersible called the "Rodpod". It's a submarine shaped like Rodimus's head. And everyone is hesitant to use it because they know Rodimus will flip out if it gets a dmaged at all.
During the tense encounter with the Necrotitan, Prowl mistakes Ravage for a dog. Doubles as a Fandom Nod towards the fact that a lot of people tended to mistake the original micro-cassette toy of Ravage for some kind of dog instead of a panther.
Prowl:"I'm with the dog."
While walking through the Dead Universe, Hardhead starts making judgmental comments about how the Lost Light crew has made virtually no progress in their quest resulting in this exchange:
Rodimus: "Yeah if you need any help hiding that disapproval..."
Hardhead: "Hey, I'm not judging!"
Rodimus: "You are judging. Orion, he is judging."
Orion: "Stop judging, Hardhead."
Dark Cybertron #5 (RID #24)
Nightbeat makes sure to thank Hardhead for murdering him.
Dark Cybertron #6 (MTMTE #25)
Getaway has incredible difficulty accepting the ridiculousness of the Rodpod. Skids ends up having to tell him to just give up on trying to understand it and go with the flow.
Hardhead attempts to bust the Dead Universe team out of a containment cube. How? Headbutting, of course! Even more hilarious is Cyclonus's perfectly timed Face Palm. It's horrifically subverted a moment later when Nova Prime kills him.
After the Rodpod's team gets lost in Metroplex, they leave the pod to explore. This results in this exchange:
Skids: No one's locking the Rodpod?
Whirl: Hopefully someone will steal it.
Then when the group ends up walking in circles and finds themselves back at the pod, this happens:
Whirl: I blame the frikken' Rodpod!
Whirl: I gotta blame something. TAKE THAT YOU UGLY PIECE OF-
(Whirl starts violently beating the Rodpod with a pipe)
Someone set up a hospital bed for a severed leg. Not the rest of the guy - just his leg.
Dark Cybertron #7 (RID #25)
When Whirl disappears from the away team (he's running after someone who tried to kill the group) this is the reaction:
Brainstorm: Something's not right.
Skids: What it is, Brainstorm? Trouble?
Brainstorm: The opposite. There's a sudden lack of tension in the room. I can't explain it.
Ratchet: It's Whirl. Where's he gone?
(Getaway's communicator rings.)
Ratchet: I bet that's him, and I bet he's done something.
Brainstorm: If he needs help disposing of a body, tell him I'm not bailing him out. (mortified)Not again.
"This scratch? I've had worse". Megatron says this in response to having his legs torn off.
Nautica and Chromia's introduction, in which they bicker over whose turn it is to make the badass threats.
Nautica: Alrighty, then—stand still, face front, hands on heads, noses where I can see 'em. If any of you speak, shrug, or sniff in a way that says "Have-A-Go-Hero," I will—I will.... <whisper> Help me out here, I haven't threatened anyone in years.
Chromia: That's why we agreed to leave the tough talk to me..."
Nautica: I know, but I was first to hit ground! I had to say something, Chromia!"
Chromia: Tell you what—ignore what Nautica's saying—and just imagine what her wrench will do to your face if you don't surrender immediately.
Dark Cybertron #8 (MTMTE #26)
Megatron tries to deliver a rousing speech about defeating the Necrotitan while making a dramatic entrance. Then Bumblebee admitted they were waiting the right moment to do it.
Prowl (to soundwave):"Unless your faith can conjure up a miracle, Cybertron is going to fall."
Megatron:"I've been called many things...but never that. Not by an Autobot, anyways."
Bumblebee:"He had me waiting there for like, twenty seconds for a dramatic entrance."
Dark Cybertron #9 (RID #26)
One conversation between Magnus and Whirl
Whirl (over intercom):"Oi, Magnus! Pick up!"
Magnus:"Whirl? What's happening down there?"
Whirl:"Your plan worked! You said that when Metroplex teleported us home he'd leave all the ammonites behind! You're a genius!"
Whirl:"P.S... (beat) I'm being sarcastic."
(cue a panel with Skids, Whirl and Getaway still fighting all the ammonites inside Metroplex)
Orion Pax' reaction to a coughing Cyclonus
Orion Pax:"Don't worry autobots —"
(Cyclonus on his knees, coughing, and clearly in pain) kaff
Orion Pax:"Sorry, Autobots and Cyclonus..."
Dark Cybertron #10 (MTMTE #27)
A conversation between Ratchet and Megatron, as the former fixes the latter.
Megatron:"I wanted to be a medic."
Ratchet:"Really? I wanted to be a genocidal despot. Funny how things turn out, isn't it?"
Dark Cybertron #11 (RID #27)
Dark Cybertron #12
A conversation between Whirl and Arcee during a fight against the Ammonites
Arcee:"Stupid, stupid minicons."
Whirl:"Ammonites. You don't have to slander the little guys"
Arcee:"There are billions of them and they're trying to kill us, Whirl!"
Whirl:"Well, yeah. No, I get that — but they're usually busy fighting their own war. They've been like super-evenly matched forever, but..."
Whirl:"A couple of months ago back I might've accidentally ramped things up a bit. I killed their enemy's leader and one thing led to another and now they're helping Shockwave kill us..."
Arcee:"Somewhere in there is a lesson about unintended consequences..."
Whirl:"Speaking of which, did I ever tell you about how I started OUR war? You'll laugh your head off."
Arcee:"You know what, Whirl? We really should've hung out more..."
Whirl reacting to the sudden demise of all the ammonites.
Whirl:"Cop out! You can't just explode! Where's the fun in that?!"
The Lost Light calling to Metroplex
Chromia:"You've reached Chromia on line 1. How can I help?"
Starscream killing Jhiaxus with his swords is equal parts awesome and humorously ironic, seeing as Jhiaxus' Adaptive Armor clued him in about the existence of his own swords. However, foreknowledge of the toy gimmick the gag is based on makes it hilarious.