As written in the Hyrule Historia, the Link in Spirit Tracks is chronologically the second Link in the Adult Timeline.
Link is originally an apprentice engineer, who becomes a hero by saving the land of New Hyrule from the evil of Malladus. Throughout his adventure, he works together with the spirit of Princess Zelda, who inhabits a Phantom form in certain situations. His appearance is similar to that of the Link from Phantom Hourglass, however, his voice is now similar to that of the younger Link from Ocarina of Time.
The game opens as Link, an apprentice railroad engineer, travels to the castle of Princess Zelda to attend a Graduation Ceremony, where the honor of Royal Engineer will be bestowed upon him by the princess herself. As she rewards Link for his service, she slips him a note, warning of the suspicious Chancellor Cole, and to take a hidden path and meet her in secret. She requests Link's help in investigating the mystery of the vanishing Spirit Tracks. Zelda is restricted to her quarters, but needs Link's help sneaking out of the castle to figure out why the Spirit Tracks are mysteriously disappearing all over the land. Zelda then presents Link with a change of clothing—the Recruit Uniform—which will help Link blend in and trick the similarly dressed guards.
After their success, the two finally make it out of the castle and bump into Alfonzo, Link's Master Engineer, who taught him how to become an engineer. As Alfonzo was once a soldier, he helps Zelda and Link escape on a train towards the Tower of Spirits. However, the tracks begin to vanish from underneath the vehicle. After a spectacular crash they are stopped halfway by Chancellor Cole and his second-in-command. The pair easily defeat Link and Alfonzo, and go on to remove Princess Zelda's soul out of her body. Chancellor Cole then takes Zelda's body and uses it as a vessel in an attempt to revive Malladus.
When Link awakens, he finds himself in Hyrule Castle. Zelda's spirit floats in, and Zelda learns she lost her body and that no one can see her but Link and a few Lokomos. Zelda then leads Link to a sword. After a bit of training she then directs Link to head to the Tower of Spirits to retrieve her body. To help Link, Princess Zelda's ghost inhabits a Phantom and aids Link in stopping Chancellor Cole and reviving herself.
With the help of the Lokomos (and Byrne later on), Link and Zelda managed to defeat Malladus as well as put Zelda's soul back in her body. With the battle over, they were soon assured by Anjean that Byrne wasn't truly dead when he sacrificed himself. She then told them more about the Lokomos as they went go back into the heavens. During this scene, Link and Zelda held hands with Link later slightly squeezing Zelda's hand.
Powers and Stats
Tier: Unknown. Likely at least 5-C
Classification: Hylian Swordsman/Engineer
Age: Appears to be about 12
Powers and Abilities: Superhuman Physical Characteristics, Magic, Master swordsman, Expert marksman, Energy Blasts, Elemental Manipulation (Via Whirlwind, Sand Wand, and Bow of Light), Resistance to Soul Manipulation
Lifting Strength: Class K
Striking Strength: Unknown. Likely at least Moon Class (Capable of breaking Byrne's guard with his sword strikes, can stagger Malladus)
Durability: Unknown. Likely at least Moon level (Survived Malladus' powers exploding out of control and the destruction of the Demon Train)
Range: Extended melee range with sword. Varies from tens of meters to thousands of kilometers with ranged weaponry.
Standard Equipment: Lokomo Sword, Shield/Shield of Antiquity, Bombs, Boomerang, Bow of Light and Arrows, Sand Wand, Spirit Flute, Whirlwind, Whip
Intelligence: Should be no less capable than any of the other Links
Weaknesses: Nothing notable