“BioShock” was a rarity: an entertaining action game that probed issues of morality, bioethics, government, personal sacrifice, religion, altruism, self-interest, class warfare, mercy, and the nature of the self with a rare depth and subtlety. There had never been any game quite like it. Even three years later, it stands alone.

Its premise was novel, offering a unique libertarian/objectivist utopia that has descended into ruin and madness. The story begins in 1946, when multimillionaire Andrew Ryan builds a city called Rapture on the bottom of the ocean. Ryan is a combination of Charles Foster Kane and Ayn Rand, and his dream is to create a society that exalts the individual, freed from the fetters of social obligations and moral restrictions. Only the individual matters.

As one might expect, narcissists unbound by the constraints of civilization are not necessarily the best people to place in a hermitically sealed environment on the bottom of the ocean. Although scientific progress flourishes in Rapture’s ethics-free environment, the populace is soon addicted to a substance called “ADAM,” which rewrites the human genome to give the user superhuman powers. People are driven mad by the constant mutations, different factions form, and Rapture explodes into revolution.

In the first game, the player character arrives at Rapture in 1960, in the aftermath of a second revolt against Ryan’s rule, and he must fight his way through the ruined city in order to solve the mystery of his own place in the story. Along the way, he faces the game’s iconic characters: Big Daddies and Little Sisters. Each Big Daddy is a hulking brute in a diving suit, assigned to protect a Little Sister. The Little Sisters are little girls, genetically programmed to hunt for “ADAM.” One of the original game’s most powerful elements was the moral choice presented by the Little Sisters: Kill them for a short-term gain (and a “bad ending” to the game) or save them with the promise of some future reward (with a “good ending”).

Three years later, “BioShock 2” recycles many of these elements to great effect. Eight years after the events of the first game, Rapture continues to rust gently away as its remaining denizens drift further into madness and various powers fight over the pieces. Sophia Lamb is now in charge of much of what remains, and her zeal to turn Rapture into a collectivist utopia has inverted Ryan’s original vision, with equally predictable results. Lamb is such a zealot that she not only has restarted the Little Sister program, but sacrificed her own daughter, Eleanor, to it.

In the years since we last visited, those remaining Little Sisters have grown into Big Sisters: lithe, fast counterparts to the diving-suit clad Big Daddies. Lamb is sending these Big Sisters to the surface to kidnap little girls, thus beginning the whole process again.

Eleanor has also grown up, and in her determination to stop her mother, she resurrects Delta, her own Big Daddy, who was killed at her mother’s orders many years ago. This is where the game begins, with the gamer taking on the role of Delta. Thus, players get to spend almost the entire game as a Big Daddy, complete with drill arm, a heavy load of weapons, and as many plasmids as you can afford. The action is a bit more to the forefront in “BioShock 2,” with a fairly steady pace of combat and more intense firefights. The Big Sisters are themselves the fiercest foes in the game. Summoned every time you save one of the little girls, they put up a tremendous fight: fast, heavily armed, and hard to hit.

The moral dimensions remain intact, leading to a slightly branching plot with four potential endings. Each time you catch one of the Little Sisters, you have an opportunity to save or destroy her. The preferred path is fairly clear, with rewards for saving the girls and a “bad” ending for destroying them. At other points, you’re given the choice to show mercy where none is required, where most games would simply require mere violence and vengeance. Your actions at these points also affect the game in various ways. It’s striking to find a game that pushes you steadily towards a confrontation with a powerful foe only to allow you (and almost encourage you) to let them live, and then reward you for doing so.

A modest religious angle has been grafted, rather ineffectively, onto Rapture. (Ryan, a militant atheist, had banned all religion and religious literature in his city.) A mad ex-priest, insanely devoted to Lamb, is a primary foe; he is used to help Lamb manipulate religious devotion and superstition in order to maintain power. It’s a concept that could have been better developed, particularly as a counterpoint to the prominent atheistic strain in Ryan’s original vision.

It’s not surprising to find a sequel that doesn’t measure up to a classic, but “BioShock 2” comes fairly close. This is an intelligent game that tackles big ideas, yet remains completely exciting. It’s also very violent, with strong language, graphic violence, tobacco and alcohol use, and sexual elements — well deserving of its “Mature” rating.

Thomas L. McDonald is editor-at-large of Games magazine