Septerra Core was a pretty formative experience from my late teenage years. (Even though it was older, I got into Total Annihilation when I was in college. Idiosyncratic purchase order for the win.)
And while I loved the gameplay and learned it inside and out*, it was the story, characters, and especially the world that had my attention.
Take the country of Jinam, for instance.
We never see the place in its glory, because it gets Doomsday Device'd before we have an opportunity to visit it. But we learn some fascinating (and horrifying) details about it from local Best Character Ever Lobo (you may want to enlarge the image, and I'll also provide a transcription because this is a fuzzy screenshot-also here's a link to the YouTube video I took the screenshot from if you want the voice acting; Lobo shows up a little after the fifteen minute mark):
(Lobo [responding to a piece of dialogue describing him as a Jinam Combat Cyborg]: "Once. I've heard that the combat cyborgs like me were made up of volunteers. But our memories were wiped clean and I don't remember. Some people have said that the Cyborg brains came from criminals, but I hope not.)
This one tidbit of information makes the nation of Jinam comparably horrifying to the main villain (who brings the world to the brink of destruction for the sake of his ego) and the undead plague that the otherwise idyllic Shell Three is suffering from. Yet other than the fact that Jinam actually is the place of origin of two party members, Lobo and that redheaded guy in the party in the screenshot, it's the most obscure location in the game, only visited once after it's been destroyed. (...And it's been wedged against Shell Three, so now it's full of zombies as well as rampaging malfunctioning robots and combat cyborgs. I don't remember the combat cyborgs there being treated as undead, but it wouldn't have shocked me.)
It's actually kind of interesting because the design of the Jinam cyborgs seems to be inspired a little by the battle droids from Star Wars (as a very slender "mook" robot), but they're basically an army of Robocops. (Despite their appearance, they're tough as nails, especially the high-level ones that pop up late in the game; Lobo is also in the running for strongest member of the party. I once saw Lobo shrug off a monster called the Hell God basically puking lava on him; he took less than twenty damage, while the guy next to him with a barrier [reduce damage by 50%, unless it was a fire barrier, which means reduce damage by 75%-I don't honestly remember anymore which it was] took nearly fifty. Granted, machine-type characters have really good fire resistance already, plus better equipment, but except for healing items being less effective for mechanical characters and the fact that he was awful at spellcasting, Lobo had no particular drawbacks [both of which can be negated by proper party composition-just stick Grubb or Led in there, and both problems are counteracted thanks to their good spellcasting abilities and Repair skills], could tank like a boss, was faster than the party average, and had high damage output and the best attack-oriented skillset in the game. The only characters who were tougher and could hit harder physically were also so slow and even worse at spellcasting.) There's apparently very little material left from the original person-the brain at most, probably not even the whole brain.
And the end result is considerably tougher than the basic footsoldiers of the Chosen, who are one of the three or four identifiably oldest cultures in the setting and usually identified as the most advanced nation (the arguable example of most advanced nation is a secret branch of the Chosen who also aren't such tremendous jerks and have turned themselves into living airships, which is awesome for reasons I don't feel the need to elaborate on). Those combat cyborgs seem to put the lie to their claims of absolute technological superiority, at the very least. (And they actually stole the strongest weapon they use, the Doomsday Device, from the Ankarans, Jinam's traditional enemy.)
If the plot of the game hadn't gone the particular way it had, there was a good chance that Jinam, not the Chosen, would have been the biggest threat to the well-being of the world. Instead, they got wiped out thanks to the main villain's machinations less than halfway through the game.
*Not saying I know everything about its battle system, but watching videos of other people playing it, well... I don't want to brag but I got pretty darned good at Septerra, to the point where watching other people play it makes me cringe**. Probably comes from playing the living hell out of the demo while waiting for it to arrive; at one point I had the party leveled up so that the toughest regular enemies in terms of the damage they could take, the Armored Crabs, were being one-shot-overkilled-for-more-than-twice-their-hitpoints by the weakest attacker in the party (albeit with his strongest basic attack). Then I got stuck on stupid puzzle junk twice in rapid succession ("rapid succession" being a period of a couple months overall) and spent that whole time randomly playing and thus grinding.
...That party was so overleveled. And yet there was a random boss you could run into that still took a tremendous effort to kill without the "cheating" method*** that kept one-shotting the party for most of the game, until I finally figured out what I needed to do ages later and came back... and took him out with a set of basic attacks. Yes, I killed the guardian of the Armstrong seal shrine once without cheating or strategy. My party was that overleveled. ...To be fair, he didn't actually have a lot of hitpoints, just more armor than a pair of battleships sandwiched together, and weapon scaling and level grinding eventually negate armor strength.
**This isn't intended as an attack on people; not everybody can spend over a year immersing themselves in every game, and Septerra was just one I spent at least a year on. ...I think I've also mentioned I'm an unrepentant level grinder; Septerra's where I picked up the habit. Also, I've seen at least one person pull a neat trick that I'd not been aware of in a video, so I won't claim I know everything. (Using Cloak to dodge the final boss's counterattack? Neat. I mean, I... kinda didn't play the final boss battle, because my sister had pushed through more of the story at some point and once she'd beaten the final boss, I didn't feel the need to-but she and I co-developed our playstyle, and she was just about as good at it as I was when we were at our best.) Actually, years later I found Chrono Trigger to be a blast because it was a quicker, less buggy version of the same gameplay, and my old Septerra habits served me well even though Chrono Trigger is a somewhat harder game; other than Lavos, hopeless fights, that room with six Nus, and a few cases where I ended up fighting high-level encounters by accident, I don't remember anything from that game as being a serious challenge.
***I mention that the boss in question, the Rot Beast, has few hitpoints but a lot of armor (pretty sure he had a lot more armor than the final boss, or basically anything but a couple of the Magi encounters), right? He's undead, so spamming the healing summon on him dealt him decent damage, but staying alive long enough to use it the five-plus necessary times was hard even though he tended to waste time reviving his zombie buddies when that killed them.
(This was a challenge because he dealt stupid amounts of damage, and had a hit-all attack that could, under normal conditions, one-shot the party. The only way to reasonably survive this attack was with the counter-undead barrier, which would reduce all damage from undead by a whopping 75%. That changed things from an impossible fight to a very hard one. He could still nearly one-shot most party members at will, though, because he had the spell Poison, which inflicted the Poison status. Doesn't sound so bad, and in a lot of games it wouldn't be. But Poison in Septerra scales in strength with the level of the caster versus the level of the victim, so instead of the percentage-based damage one might expect, or something piddling and annoying, as soon as the poison kicked in your character was dead even through a barrier, because poison damage and barriers don't interact and that Rot Beast had a ridiculously high level. That bastard was scarier than Draxx, the godlike necromancer who presumably created him and all other Beast enemies [and also happened to be the first Beast you encounter], who were generally a sort of miniboss archetype who were also occasionally storyline bosses. Compared to Draxx and the Rot Beast, the other story boss Beast, the Curse, was kind of a joke, though, because even though he was statistically stronger than Draxx, he had an AI bug that would make him spam the Curse spell if you set up a Ward barrier and made sure the party was cured of Curse. Free tip if the guy ever gives you trouble.)
Giving him a healing item, though, did fixed damage to him equal to the healing value of the item, and I'm pretty sure that the Root, which would long since have become one's standard healing item, does more damage to him than his total health (or close to it, failing that), and I know that the next item up on the scale would do him in. The game designers clearly didn't see this as "beating" him, though, because if you use healing items on undead, you don't get any experience.
By the way, I did kill the Rot Beast the hard way more than once. After all the grief he gave me, I felt the need to.