General Facts
Maelstrom Prison is a Republic-only launch flashpoint originally designed for levels 35-42 and forms the second part of the Jedi Prisoner storyline, which is connected to two additional flashpoints on Empire side. It had a hardmode from the beginning and was given a solo mode in 4.0. Nowadays it's yet another tactical (role- and level-neutral) flashpoint available from level 15 onwards.
The story that began with Taral V was that a mysterious Force ghost had spurred Jedi Master Oteg into action to seek out the Empire's secret so-called Maelstrom Prison, where a mysterious Jedi is being held prisoner who is apparently very important to the Republic. In Taral V you needed to fetch a
Fights
The Maelstrom Prison is a huge complex, to the point that it seems a bit nonsensical to have a facility that size for a single prisoner, no matter how powerful he is. To populate all those rooms, it's not just filled with Imperial guards and droids, but also with a fair amount of Sith and a number of random beasties that were presumably being experimented on or something.
Gameplay-wise there's nothing very challenging about any of the trash, except for a couple of pulls that can be painful for a low-level or otherwise badly balanced group due to the sheer number of mobs they contain.
The bosses are split about fifty-fifty between boring and interesting.
In the "boring" column we have the first boss, a droid whose mechanics I'm not entirely sure about to this day. Are you supposed to run away or stack up when he does his smashy move? Who can tell? It's not as if it does enough damage for it to make a noticeable difference either way. Then there are the two Sith dudes with pets (one just has one, the other summons several weaker ones) that also do nothing really interesting, except that one of them has what I consider to be the worst voice acting in the game, which never fails to make me giggle. The three elite guards near the end used to be somewhat interesting back in the day because they can't be crowd-controlled and hit very hard, which means that you used to run the risk of your tank turning into paste before you could kill the first of them off, but they aren't really the threat they used to be.
In the "interesting" column, we have Colonel Daksh and his eye beams of doom. I'm actually not entirely sure how the 4.0 rebalancing has treated him - in tactical mode he still hits very hard for what is supposed to be role-neutral content, but I don't know how hardmode has been retuned. Either way, this boss is quite interesting in that every so often he will "charge up his ocular implants" and basically turn them into lasers that hit so hard that he becomes pretty much untankable, forcing the tank and possibly the rest of the group as well to do a little dance around a nearby stack of crates until his implants run out of power. Threat is very tricksy during this time, since the tank can barely generate any, but many a dps risks overaggroing anyway while the tank is kiting - better hope the boss doesn't suddenly turn around!
Then there is the bonus boss, a giant Maelstrom beastie, which is available on all difficulties. It's not really that interesting in terms of mechanics except that it has a huge knockback that can send unwary party members flying off a nearby ledge to their deaths. However, I've always loved it simply because it's so damn impressive when you release it from its prison. The only issue right now is that Bioware forgot to add kolto stations to the area where you have to fight it when they did the big 4.0 retuning, which means that the fight is pretty much impossible without the right group composition, as the boss just does too much damage. Funnily enough, the only time I've beaten this beastie on tactical since 4.0 has been when I was duoing the instance with a dps while on my tank (the other two players had rage-quit after we had wiped on Daksh), and both of our companions were set to healing stance.
Finally, we have the final fight of the instance, Grand Moff Kilran, who makes all snipers wish that they could be as powerful as he is. Basically he has some bodyguards that first make him immune to all damage until you kill them, and he applies a huge area slow that makes it hard to get into melee range with him. Yet until you do so, he will keep casting sniper abilities that do massive damage if you don't manage to avoid most of his shots by hiding behind nearby pillars at the right moment. Once you've got him down to half health, he will retreat to a position further back where he will once again start sniping until you can get into melee and/or kill him. Again, quite an interesting and also challenging fight.
Story (spoilers)
You successfully infiltrate the prison with little fuss and Oteg poses that you've managed to actually surprise the Imps. However, about halfway through the instance, Grand Moff Kilran of Esseles and Black Talon fame shows up once again (you had spoken with him in Taral V as well) and has a fleet at his back.
Oteg states that the mission is important enough that sacrifices need to be made and says that he will use the Republic fleet to stall Kilran. You can agree to this (dark side) or urge him to take as many people as possible to safety because you'll be fine anyway (light side). If you take the dark side option, Oteg fights valiantly but dies during the engagement.
As you approach the "cell" of the Jedi Prisoner, Grand Moff Kilran shows up in person to stop you. You can see him talking to Darth Malgus on the holo and vowing to protect the prisoner. Of course you take him out anyway, but as I said above he actually puts up a pretty good fight.
Finally you are able to release the mysterious prisoner and it's... Revan? He's actually not particularly happy to be freed, because he claims that his influence on the Sith Emperor - even while he was being kept alive as his prisoner for hundreds of years - was what enabled the peace between Republic and Emperor. The mysterious Force ghost that you met in the intro to Taral V shows up again, clearly a friend of Revan's, though their relationship isn't explained.
You successfully escape the prison and in the debriefing on the Telos, Revan explains that he has grand plans to stop the Empire, which involve a secret facility called the Foundry.
Conclusion
In my post about Taral V I said that it was one of those early flashpoints that left a deep impression on me, and Maelstrom Prison was an even stronger follow-up to that, even if its environments are a little more bland overall. Finally offing Grand Moff Kilran after having engaged in verbal sparring with him in several earlier flashpoints felt very satisfying, even if in hindsight it was maybe a bit of a waste to have him die that early in the game as he was a pretty fun villain.
And of course... Revan! Though there is the problem that nothing is really explained after the big reveal. If, like me, you hadn't played the KOTOR games (yes, so sue me) and didn't really know who he was, there wasn't much opportunity to get clarification. The identity of the Force ghost who started the whole thing isn't even touched upon; it was only after I read the Revan novel that I learned that it's supposed to be Meetra Surik and who she is.
The worst thing about the storyline however is that it ends with Revan confirming that he is apparently as big of a deal as Oteg claimed, that he thinks he has the key to defeating the Empire, that he hopes to meet you again some day... and then you never hear from him again (as a Republic player anyway, not until Shadow of Revan, and then you're kind of like "wait, what?").
Even so, I still consider infiltrating the Maelstrom Prison a great adventure and would recommend to anyone to at least check out the new solo mode now if you missed this storyline back in the day because you were too shy to run group content. It works particularly well if (unlike me) you read the Revan novel first.