Mission 6, Kazuma's first awesome moment: taking on a Tekkaman essentially single-handedly in an industrial loader for several minutes while Milly finishes Pegas so that D-boy can tekset again.
The entirety of Mission 12: Several of the teenaged members of Warter (The Heroes' group) end up enrolled at Kaname's school (As if Sousuke wasn't bad enough). Meanwhile, Kaname is given the task of doing something about the school's perpetually-losing Rugby team plus finding something entertaining for the School Festival, not to mention making sure delinquents from rival schools don't mess things up. Naturally, she enlists Sousuke's help, despite the fact that she really should know better by now. He tells her that he'll handle the whole load himself. The day of the festival comes, and Baron Ashura decides that (s)he'll strike at Kouji Kabuto, the pilot of Mazinger Z, by attacking the school with a pair of robot beasts. But when the attack begins, Sousuke reveals the re-trained Rugby team, all equipped with Bonta-Kun suits! After getting the team Psyched up (With Kaname translating a surprising amount of foul language, in front of children, no less), they proceed to blow the two beasts straight to hell. When Death Black Beastmen and fighters from the Galra Empire show up, Sousuke has a plan for that too. To keep the illusion that this is All Part of the Show, he has the Bonta-Kuns direct giant magic lions (namely, GaoGaiGar and Voltron Golion) to protect the school. Much asskicking ensues, leaving Baron Ashura with a healthy fear of Bonta-Kun from now on.
The second time you play it, it involves the "Beauty Contest" episode from Martian Successor Nadesico. This time, Ashura desguises his/herself as Dr. Yumi to try to sabotage the proceedings and get someone incompetent selected as captain. (s)he gets Yurika (re)picked, of course. Angry that didn't work out, Asura summons a pair of robot beasts to attack, only to find out that Sousuke's contribution to the "keep rival delinquents out" plan just happened to have included enough high explosives to kill two robot beasts outright. The following mission includes a major beatdown of a rival military squad with a team of Bonta-kuns, and the subsequent humiliation of Pizza by the same.
Mission 15 of the same: "Five-Colored Bonds, Gold-Colored Hero". Sven/Shirogane's just been badly injured killed, and the VoltronGoLion team has spent the last week trying to train the princess to take his place in the blue lion with limited success. Allura Farla's doing well, actually, but the blue lion's just not responding to anything. To make matters worse, GaoGaiGar's "Hell and Heaven" Finishing Move is taking a near-fatal toll on Gai's cyborg body. But there's no time to work things out just now and you have to sortie with both GaoGaiGar and GoLion benched for the time being. Our heroes find themselves confronted with the sight of three Tekkamen chasing a fourth. It's D-boy's sister Miyuki, and if you've seen the series, you know where this is going. To make matters worse, the Zonder show up, intent on taking Miyuki for themselves and finding out how the Tekkamen can resist Zonderization. They capture her and trap her within a Zonder, triggering a three-way battle. GaoGaiGar sorties, Guy being more than willing to sacrifice himself if he can save Miyuki. Here's where the awesome kicks in: Trying to make a bad situation worse, Haggar Honelba infiltrates the Nadesico in order to kill Farla, but she's stopped when Mamoru, of all people, forces her off the ship. Honelba turns her wrath on him, but is stopped when Farla gets the Blue lion to move and attacks her. The others also quickly sortie, and GoLion is back in the fray. With the Zonder and Radam chased off, that only leaves the problem of Miyuki. Gai begins to power up Hell and Heaven, over the protests of everyone, including D-Boy, when Goldymarg shows up to lend a hand (and a Big FraggingHammer) HIKARI NI NARE!!. GoLion and GaoGaiGar are back in business, Miyuki is safely within GGG's care, and one of the most tragic moments in Tekkaman Blade is completely temporarily averted.
As much as awesome that scene is, however, it's still possible to re-enact the tragic moment, if you didn't focus much on the Tekkaman Blade scenario. Miyuki can still permanently die, but through another method.
IIRC, She survives that, too. She helps Blade get out of the path of a Wave Motion Gun (explained below) and uses Shinya's crystal (since he didn't need it to get to the moon here) to restore the mental degradation he was going through at that part of the series.
Stage 37 of Paris route,The Final Battle against Mycene. As a bonus it also includes the awakening of Kaiser Nova, Shin Shine Spark, And new combination attack, including the FINAL DYNAMIC SPECIAL against Ankoku Daishogun.
Stage 45 Mars route, Creuset puts Flay in an automated GINN along with the blueprint for N-Canceller, and sends them towards the O.M.N.I. Enforcer and the protagonists. However, unlike in canon, the Dominion is forced to retreat before they can recover Flay. Just as Kira is about to save Flay, Creuset shows up again and tries to shoot her like he did in SEED's finale, but the Eternal of all things rushes in and takes the shot, saving Flay from her canonical death.
Stage 49 is filled with awesomeness. Other than a small twist from the original (you didn't enter another dimension), Guy recovers from Sol Lords' control and receives Genesic Gaogaigar, and asskicking ensues. But Valzacard's debut tops that off: After Kazuma, Mihiro, Aria and Regulate with Alm Stola escapes from The Database's station, they're under hot pursuit from Applicant and his brand-new Alm Stola Finis, it's at this point Horace announces "all keys are gathered" and execute the combination code. Cue Sail for the Future and watch Kazuma piloting Valzacard to kick Applicant's ass.
After Stage 49, the good guys have to split up, half the force going to take on the Radam on the Moon, and the other half to stop GENESIS. On the Bloody Valentine War side, the heroes have managed to take control of the station, but the weapon is already charged up, and they don't have the time to stop it. That's when Ruri calls in from the Nadesico C and hacks the control system to point GENESIS at the Radam command ship as it takes off, killing two birds with one stone.
The Radam path was pretty badass too - you go through the Tekkaman Blade finale mostly keeping to canon (with the usual accounting for SRW craziness)... but when D-Boy loses his personality and memories, running purely on hatred for the Radam, leaving Aki to mourn his cruel fate to fight alone... Ruri chimes in out of nowhere with a "He's not alone." and jumps down with the rest of the gang, ready to rip Omega and the Radam remnants a new one. They then all proceed to call out to D-Boy, and end up dodging the Bad End the anime had by having D-Boy reclaim himself and then proceed to beat the living shit out of Omega.
Also, Blade and Evil having a final duel in Stage 50. Alone. Kill him and he transform into Blaster form, and so does Blade. And they have a second duel. All while Masquerade is playing as the BGM. Its as awesome as it sounds. It's also a Tear Jerker since, having a twist from the anime, Shinya/Evil is able to revert back to his own personality and helps D-Boy/Blade to break out from surrounding Radam Beasts, ending the stage by blowing himself up along with all "enemies" around him.
ZAFT route is no slouch either. Gai Murakumo breaks into the bridge of the Dominion in Stage 50, delivers an epic beatdown to Azrael (including a Shout-Out to Rom Stoll), and evacuates everyone (including Natarle) from the ship, leaving Azrael to die alone. Due to this twist, Mu's life is also spared, and this directly leads to Colbert's death.
In the same stage, the Sol Lords decides to attack Nadesico A (with Yurika in command, it's a long story) directly and Akito, who ran away again after Stage 47 (the last of The Prince of Darkness storyline), shows up and rejoins your group ,vowing to protect everyone. After this, go ahead and strip all of the armor and extra weaponry off his Black Selena, and perform the Double Gekigan Flare with Gai Daigoji once more.
Extra points: try to notice what he says during said attack (Except he went completely silent). He hasn't lost a bit of his hot-bloodness and love of justice even after all the hardness. For another proof, let him attack Syncline in Stage 54———he'll pick up the old thoughts of "Justice will always prevail over Evil" like he was in the TV series.
Prior to Stage 54, your group is desparate to find The Database's main base among the stars. So how do they find out? Remember Kaname stays behind when Sousuke rescues Tessa in Stage 49? She uses Whispered's resonance to tell Tessa about her whereabouts (in The Database's main base on Pluto), and as Taiga puts, the girls risk their sanity to bring the news to the group. Sail for the last battle!
Hats should also go to the script writer, who is able to incorporate the real-world news of "Pluto being demoted to Dwarf Planet" around that time into the game and makes it a major plot point. (Lampshaded that way long before this event, everyone tries to recall the "forgotten planet" in the Solar System but no one remembers)