SPOILERS OF EACH
Prototype and Prototype 2
The story for me was really interesting as Alex Mercer tries to find out what he truly is and why he turned into the monster of a man who can create weapons and see the memories of people he consumed and killed. When he does finally find the answer that he's not Alex, but a Virus that takes the form of Alex Mercer with his memories and emotions, he starts to actually go a bit insane in the second game and recreate the world by killing off humans. Of course he also infects James Heller to ask him to help destroy Black watch, the people responsible for Alex's transformation and the outbreak of infected. But James catches on and decides to hunt and kill Alex Mercer in order to save his daughter an the city as well. The story really puts a big question on a person's true humanity and gives a very entertaining cast of characters as well. Plus the sheer free for all in killing people and infected is almost too fun to deny.
Assassin's Creed II
Assassin's Creed II was my first Xbox 360 game as it follows the story of Ezio Duditore Da Firenze, an Italian man of the 14th century who witnessed the death of his father and twin brothers by a ruthless cult of Templars who planed on world domination. Now it was up to Ezio to done the Assassin's white robes and wrist blades to kill the Templar order and save Italy from their twisted plans. I really enjoyed AC2's style, music, setting, and all around story telling along with its gameplay. It definitely has the title of best AC game all around in my book.
Persona 4
Persona 4 in my opinion had a very cool and slice of life/adventure story as it follows an silent protaganist (Yu Narukami as I like calling him) and him moving to a quiet little town called Inaba, where he meets friends and has a normal life...until his television tried to eat him. Since then strange things have occurred from a corpse on a TV poll to strange disappearances all over Inaba. Yu and his friends are now on the case as they travel into a strange alternate world where they must use their ultimate beings called "Personas" to defeat the darkness that covers the alternate world and save the human realm from falling into chaos. I've not played the game yet but I have seen cutscenes and gameplay walkthroughs and I must say its very unique and greatly detailed in a lot of elements.
DmC: Devil may Cry
Now I know how "controversy" the game is, but I just love the story. For those who don't know (and obviously you all do) I'll just explain it; The story follows Dante, a young rebellious individual who enjoys pizza eating, drinking, and having casual sex with strippers and whores. However he also has a darker secret going on with him; he can see and fight demons. He uses a trusty sword and twin pistols to kill and destroy his demon foes from killing him. But one day, he meets a girl named Kat who invites him to take part in an organization called "The Order" who's sole purpose is to destroy the demons once and for all while the leader, Vergil runs it who is also Dante's long lost twin brother. Now Dante must defeat the demons with the order in order to take down the demon king Mundus and save humanity from the demon's grip. While going through all this, Dante must also come to terms with his true power and accept his true nature as Nephilim; a hybrid of Angel and Demon. This story was unique compared to the other DMC's of the series and I really did enjoy it. It had a cool level setting and its gameplay was a unique spin on the series but still keeping what made DMC cool.
No More Heroes
It was one of the most crazy and hilarious games I've seen. It's a story about Travis Touchdown, a man who's out of money and needs it fast. So what other way to make quick money then to be an assassin. However, he then gets caught up in an insidious game created by the United Assassins Association, or UAA where he'll have to kill all the top ranked assassin's in order to be number one, where both money and a promised good time with the head director Sylvia Crystals was waiting for him at the top. It's definitely a game that doesn't bore you that easily. With its fun characters, straight forward plot, and hacking and slashing, it's definitely a good one.
Lollipop Chainsaw
This crazy game is about Juliet Starling, a teenage cheerleader who just turned 18. However her birthday is filled not with cake and balloons but blood and dismemberment. On her very way to school, she comes in counter with a horde of zombies that threaten the entire school to get infected and become zombie slaves. And then there's the zombie leaders who control different parts of San Romero school and the very city as well. Now it's up to Juliet, and her decapitated living headed boyfriend, Nick to kill all the zombies with her customized chainsaw and her zombie hunting bloodline and save humanity from eternal enslavement form the zombie new world. No big deal. I really enjoyed this game for its comedy, action, and music choices. It may not be the best Suda 51 game, but it's certainly the biggest one to leave an impression.
Kingdom Hearts 1
This is still the best one to me. The story is about a young boy named Sora who lived on an island with Riku, and Kairi. They all wanted to escape the watery prison of an island and go out to sea to see other worlds that could be out there. They get their wish, but in a bad way when the island is being destroyed in darkness and dark creatures appear. Riku escapes by excepting the darkness, while Kairi is taken away and vanishes from Sora. However Sora was also able to escape and wound up in a sleepy town where he meets two guardians of the King of Disney castle Donald the wizard, and Goofy the guard. Sora must now travel with these two and fight the darkness with a magical key sized sword called the keyblade and travel to different Disney worlds to find Sora's friends and save the worlds from darkness. KH1 to me was the best out of all the KH games. It had that great character development, and the walk down memory lane of all my favorite Disney characters is something that I enjoy. Along with its gameplay KH as a whole is a very complex story that is hard to follow if you haven't played all the games, but once you do, you'll be happy you did.