Caretaker I & II

In the very first Voyager episode, we find out that Chakotay and Tom are already acquainted. They were in the Maquis together. And when Chakotay sees Paris aboard Voyager after finding out that Tuvok was a spy, he's livid.

Chakotay: "I see you had help."
Tom: "It's good to see you too, Chakotay."
Chakotay: "At least the Vulcan was doing his duty as a Starfleet Officer, but you.. You betrayed us for what? Freedom from prison? Latinum? What was your price this time?!"

When the crew is ready to head over to the array, Tom catches up to the Captain.

Tom: "Captain! I'd like to go with you."
Janeway: "If this has something to do with what Chakotay said.."
Tom: "It doesn't! I just.. I'd hate to see anything happen to Harry."
Janeway: "Come on."

In part two..

When Kes, Neelix, Torres, Kim and Paris make it safely to the surface of the planet, Tom finds that he needs to go back and help Janeway, Chakotay and Tuvok. Neelix goes with him. Neelix helps Tuvok reach the surface, and Tom helps Chakotay as the stairs are being destroyed all around.

Chakotay: "Get out of here Paris, before the whole thing comes down."
Tom: "I intend to. As soon as I get you up."
Chakotay: "You get on those stairs, they'll collapse. We'll both die."
Tom: "Yeah? But on the other hand, if I save your butt, your life belongs to me. Isn't that some kind of Indian custom?"
Chakotay: "Wrong tribe."
Tom: "I don't believe you."

He finally reaches Chakotay and helps him up from the partially collapsed stairs

Tom: "You'd rather die than let me be the one to rescue you?"
Chakotay: "Fine, be a fool. If I have to die, at least I'll have the pleasure of watching you go with me."
Tom: "Isn't there some kind of Indian trick, where you can turn yourself into a bird and fly us out of here?"
Chakotay: "You're too heavy."

When the Kazon begins to attack Voyager to try and keep them from transporting over to the array, Chakotay is on the Maquis ship and has a plan to fly directly into the Kazon ship to destroy it. He's getting very close to impact, when..

Tom: "I'm getting you out of there, Chakotay."
Chakotay: "Not yet."
Tom: "You're breaking up. Standby to transport."
Chakotay: "Wait!"
Just as the ship collides with the Kazon, Chakotay is being transported.

Chakotay: "Now!"
Tom: "Transporter room two? Do you have him?"
Chakotay: "They've got me."

At the end, Janeway tells Paris that she has invited the Maquis to stay aboard and serve, and that Chakotay is now her First Officer. Tom cracks something about needing a bodyguard, but Janeway tells him that Chakotay mentioned that his life belongs to Tom, so he'll personally be responsible for Tom's safety.