Warning: Jak 3 ending spoilers. I tried to mark them but this subreddit doesn't support any way to mark spoilers.
In jak II, you meet younger jak. How is this possible if the game takes place in the future? There's two jaks existing at different ages at the same time. How's that possible?
Both Jak and Samos were originally born in the future, in the world where Jak II takes place, and it is here where Jak exists as a young boy.
At the end of Jak II, the younger version of Jak and the younger version of Samos are both sent through the rift gate into the past, to the world where Jak and Daxter: The Precursor Legacy takes place.
Then, once Jak has grown older, Jak and Daxter: The Precursor Legacy begins. At the end of the game (which then begins the start of Jak II), Jak rediscovers the rift gate he used to travel to the past and uses it to accidentally travel back into the future and into the world in which Jak II takes place.
This is now the second time that Jak has lived through the events of Jak II; the first time as a young boy, and the second time as an older version of himself after the events of Jak and Daxter: The Precursor Legacy. This is why there are two Jaks in the same place and time.
Basically, the games in chronological order for Jak are as follows:
One, Jak II: Where Jak is born, as the son of Damas. He then goes through the world as a young boy, before going through the rift gate at the end of the game, along with the younger version of Samos.
Two, Jak and Daxter: The Precursor Legacy: Where Jak enters into Sandover Village through the rift gate from Haven City as a young boy. Then, after Jak grows up, Daxter gets turned into a precursor and Jak proceeds to defeat Gol and Mia.
Three, The first five minutes of Jak II: Where Jak and his friends from Sandover Village rediscover the rift gate and are accidentally transported into the future. Then, Jak is taken prisoner and experimented on using dark eco, meanwhile separated from Daxter.
Four, Daxter: Where Daxter goes on an adventure to find Jak.
Five, Jak II: Where, after Daxter finds him, Jak escapes from his prison and proceeds to carry out the events of the Jak II game, whilst also guiding his younger self and the younger version of Samos through the rift gate at the end of the game.
Six, Jak 3: Which takes place after the events of Jak II.
Seven, Jak X: Combat Racing: Which takes place after the events of Jak 3.
Eight, Jak and Daxter: The Lost Frontier: Which takes place after the events of Jak X: Combat Racing.