Separate Ways is a bonus game in Resident Evil 4 HD and in certain RE4 releases. In it, you play as Ada Wong as she goes through the events from the main game. You will come across Leon Kennedy a few times through the missions.
The story begins with Ada in the village centre; after fighting off a pair of Ganados, Ada is instructed by Wesker to ring the church bell, in turn pacifying the villagers. At that time, she notices Leon having troubles of his own, ambushed by a gang of villagers. Racing to the church, Ada discovers the door locked. The round insignia needed to open it is around the back, protected by a dial puzzle. Although she solves it, something must be placed in the mechanism to keep the gate behind her open. Heading along the shore, Ada encounters one of the Chainsaw Sisters. After defeating her, Ada retrieves the Green Catseye, returns to the church and solves a puzzle to retrieve the Round Insignia, then switches it with the Green Catseye. She uses the Insignia to enter the church, then solves the light puzzle later seen with Leon to ring the church bell, although bringing down the steel bars that prevented Leon from getting to Ashley.
Reading a book about the villagers in the home of Bitores Mendez, Ada gets a call from Wesker to inform her that the researcher they planted, Luis Sera, has been captured by Mendez and is being held in a house on the other side of the village. Until he obtains the control plaga sample for them, he cannot be allowed to die. Ada remarks that Sera is quite high-maintenance and sets out to rescue him.
After fighting her way through the village, including Chainsaw Man, Ada arrives at the house only to find that Leon has also been captured and that the Ganados are moving both prisoners to the valley.
Racing back, Ada arrives at the chief's house just in time to save Leon from a quick death. However, this causes Mendez to chase after her instead. Eventually, Ada is tranquilized and captured.
A few hours later, Ada wakes up just in time to avoid a grisly death at the end of a Ganado's axe during an Illuminados sacrifice. She makes her way up to the lift control room to discover that she needs a key to activate the gondola lift. She goes to the barn where, in a few hours, Leon will face off against Chief Mendez. For now though, there are only a few villagers, including a second Chainsaw Sister who is possession of the key Ada needs to advance. Defeating her opponents, Ada uses the lift and proceeds on.
However, there is one last obstacle in her way: El Gigante. Either by fighting or fleeing, Ada gets past the monster arriving just after the siege on the cabin has ended. Luis informs her that he's on his way to get the sample. He asks her who she works for and she replies that there are things he's better off not knowing. He says he doesn't really care who she is as long as she gets rid of Saddler and the Los Iluminados.
The chapter begins with Ada revealing herself to Leon and escaping into the hedge maze. Wesker calls her with important news: Luis has gotten his hands on the sample. Ada is to track him down and get it from him. Additionally, if Ada encounters Leon, she's ordered to take him out. He's a survivor of Raccoon City, Wesker says, they can do without the distraction.
The sudden arrival of the cultists somewhat hampers Ada's efforts to escape the maze, but she makes it with little difficulty. Making her way through the castle, including a fight with a Garrador, Ada stumbles upon Leon and is unable to help him as she'll have to kill him if he sees her.
Eventually she arrives at the meeting point only to witness Saddler kill Luis and take back the sample. Wesker calls, telling her that they might be able to use Leon as a distraction to harass Saddler and his men. Unbeknownst to Wesker, Ada's been doing that all along.
Krauser and Ada meet at the island's radio tower. Afterwards, Ada gets a call from Wesker informing her that he's dispatched Krauser to kill Leon. Ada reminds herself that she doesn't always play by Wesker's rules.
Finding herself in the shipping lane from the waste disposal center, Ada goes on the offensive through hordes of soldiers, even going so far as to sink the warship that Saddler has somehow recommissioned all by herself (she even used a pair of Gatling cannons to destroy the warship's onboard artillery).
Arriving at just the right time of Leon and Krauser's knife battle, Ada shoots Krauser's knife out of his hand as he is about to stab Leon in the heart and he is forced to flee.
As Mike and Leon decimate the military base, Ada informs Wesker that Krauser has been killed. Impressed, Wesker remarks that Leon doesn't die easily. He plans to use Leon to take care of Saddler. No matter who wins, the victor won't emerge unscathed and he instructs Ada to finish off whoever is left. Neither Leon nor Saddler can live to see tomorrow.
Clearing out what remains of the mercenary defenses, Ada meets up with Leon just in time to witness his Plaga try to assert itself. Going on ahead to let him compose himself, she defeats the meager resistance in the cell block. But as she's about to advance, she is nearly killed by a girder.
Krauser, badly burned and injured, had survived both Leon's assault and the explosions that destroyed the ruins and he intends to pay Ada back for her earlier humiliation. However, Ada has carefully studied his fighting style and, despite his arm, she is able to overcome her old ally, killing him for good.
Immediately after, Ada arrives in the laboratory to distract Saddler, giving Leon the precious time he needs to rescue Ashley and escape. Unfortunately, she must now fight the deranged cult leader. Through a combination of wits and firepower, she is able to defeat him and finally gets her hands on the control plaga specimen. But she does not see one of Saddler's tentacles and is captured.
A short time later, Leon arrives on top of the structure where Saddler and Ada are waiting, Ada tied and hanging from a rope. Leon cuts her down and begins to fight the mutated Saddler. Ada, seeing a rocket launcher on another structure, goes on an all-out offensive, racing against both a swarm of Ganados and the timer of a great number of bombs. But she overcomes every obstacle, retrieving the launcher and, in a parallel of the same event six years earlier, tosses it to Leon at the last moment.
Holding Leon at gunpoint, she finally retrieves the plaga sample. Tossing Leon the key to a jet-ski, she takes off in her helicopter just before the island is destroyed.