Hey, Hey! Listen!

"So,
I've got a friend. You haven't met him yet, so I'll tell you about him.
Hey, are you listening? I'll quiz you! Sound fair?

This guy, he's a bit of a trouble maker. At work, when something goes wrong, we can take a guess as to who the cause of it was. He's a young recruit to our IT department, and he can cause quite some havoc to our directory. He's a good boy, though. His house plants are all alive because of him. Oh, right! Originally we accepted him into the Finance department because he was good at math, but it turns out he was really square about his methods, so we put him in IT instead. Good lot that did us, huh? Anyway, where was I... ah, yes- even though he's in IT now, his behavior from Finance stuck- I guess he's really set in his ways... something we should have checked for before we hired him.

Okay, I think that was enough of an introduction... so, were you listening?
Were you really? Then, what's his name?"

Hint 1:

His name correlates to every italicized section (as guessed in the comments)- either replacing the word or adding to the word to form a different meaning. For example, walking could become walking stick: the meaning changing from "to go" to "an aiding item".

Hint 2:

The word that fits the bill is 4 characters in length.

• I bet his name is @iiiidk, that trouble maker Aug 9, 2018 at 21:01
• =honk honk! That's me! :^) Aug 9, 2018 at 21:01
• How many puzzles do you create a day?! Aug 9, 2018 at 21:04
• @Joe-You-Know iiiidk :P Aug 9, 2018 at 21:05

I Think it's:

Root

Root cause
Root directory
Him root(not sure), maybe root him :) roots
set root

• My guess at the sentence 'His house plants are all alive because of him' refers to rot13(gur cynagf ner fgvyy nyvir orpnhfr gurl unir 'ebbgf'). as stated in the hint it could also replace. Aug 13, 2018 at 10:17
• @mrdeadsven Yeah, probably. My English is not that great :) I thought it was a word that I didn't know. Aug 13, 2018 at 10:57
• Wonderfully done :) The wording that makes the most sense to me for the last two are rot13("ebbgf" naq "ebbgrq")- as mrdeadsven mentioned. Aug 13, 2018 at 14:01

I'm not entirely sure why I believe this, but I think his name is

The title is a dead giveaway: Hey, Hey! Listen! refers to

Navi, from the Legend of Zelda and the Ocarina of Time.

This guy, he's a bit of a trouble maker.

Link is based on Peter Pan, who was in turn based on Pan, a god of woodland mischief.

At work, when something goes wrong, we can take a guess as to who the cause of it was

I believe this is referring to Mido and Link, and Link being responsible for killing the Deku tree.

He's a young recruit to our IT department, and he can cause quite some havoc to our directory.

Link kills a bunch of plants, steals a sacred Kokiri sword, among other things.

He's a good boy, though. His houseplants are all alive because of him.

He saves the forest by killing the spider thing.

Originally we accepted him into the Finance department because he was good at math, but it turns out he was really square about his methods, so we put him in IT instead.

I think this is referring to some sort of video game maybe, Four swords to make a square, maybe?

I guess he's really set in his ways... something we should have checked for before we hired him.

He gets reincarnated each game.

• I was thinking the same thing, but what does it have to do with the body? Aug 9, 2018 at 21:06
• @Cubemaster, I'm 90% sure that you are right, but I thought I'd have some fun with this answer. Aug 9, 2018 at 21:13
• Oh yes, it does @Cubemaster . Now that the explanation is there... rot13(V'ir arire cynlrq gung senapuvfr, ohg V QB xabj bs Aniv, ohg vg unf ab eryngvba- vg jnf whfg gb rkcerff gur tebff punenpgre bs gur fcrnxre.) I know I know, crazy right? How did I have a childhood? Aug 9, 2018 at 21:14
• Go out and buy you a Legend of Zelda game. I am a grown man and I still play the hell out of that franchise Aug 9, 2018 at 21:19
• I grew up with a Link to the Past on the snes and with Ocarina of Time on the 64. I took up speedrunning because of those games... Sigh, nostalgia. Aug 9, 2018 at 21:21