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There is no one definite answer to this topic. And most likely never will be. However, various side materials allow us to make educated assumptions and throw away some of the early theories.
- In English there are quite a lot of 4-letter words. Most players thought of (and rightfully so) about the f-word. Others suggested that it is kill.
- In Japanese an obvious word might be kill/destroy for some people. However, rape/violate fits just fine too. Furthermore, with how the phrase is hidden there are literally hundreds if not more of possible kana/kanji combinations.
There is a possibility that 8-4 decided to put a clever meta joke where there was none in the original. But not only Yoko Taro knows English a bit, but both English and French translations were used in the official Strategy Guide (although some of the localization quirks also made its way there). Also, during Dinner Spoiler Talk Show there were some jokes made about this line.
Could it be censoring?
Yes, there is also a possibility of that. Some may say that in the English version of the game the f-word is used openly once - in the Jackass Machine Research Report. However, in Japanese there is no swearing involved in that doc making Adam’s line fittable for censoring. Furthermore, in NieR Replicant, Kaine’s swearing was censored the same way in subtitles.
So what's the word?
Strategy Guide sheds a lot of light into what 9S was actually thinking while being mind-raped by Adam:
Adam’s speaks of truth. A far too inconvenient truth for us.
Stop it. Don’t look. Don’t open me up. His tormenting series of words ravage my mind, and I feel as if my entire existence is being violated. The words of despair that Adam whispers at me tore at my body with an even greater pain than my impaled limbs, and I feel my existence being laid bare before him. The pleasure of humiliation and violation a searing pain upon me.
“Emotions are prohibited.”
Just because they’re prohibited, doesn’t mean they’ll just up and disappear by themselves. Right, 2B?
“You do not trust anything.”
“You want to destroy everything.”
“You have lost hope in everything.”
“You want to obtain everything.”
“You want to be loved by all.”
“Emotions are prohibited.”
If I smother these feelings of mine that just won’t go away and hide them deep within my heart, will I get to always be by your side, 2B?
“You’re thinking about how much you want to **** 2B, aren’t you?”
I opened my eyes when released from my imprisonment, and see that she has come to save me. I have never been so thankful for my goggles before. I am so glad that I’m too injured to form proper words. If emotions are only expressed with my eyes and my voice, then this will keep her from finding out. I remain silent. I hid away these filthy thoughts of mine...because humanlike emotions are prohibited.
(Yes, the section about Adam’s mindrape is supposed to be extremely suggestive, because that’s what it is.)—Strategy Guide/Game Chapters Comments 
This segment alone as well as general context at that point of the game and what happens next makes it clear that kill is not a fit.
That said, in A Long Story:
"his wicked feelings were peeked into [by Adam]"—A Long Story/2B, 9S, plot content Q&A 
And the overall possessive behavior of 9S towards 2B in the later Route C might suggest that word is to own (directly fits only in Japanese). But doing such a wild comparison between 9S in route A/B and his very complicated situation in Route C is unreasonable.
In the game (but for some reason not in A Long Story) Adam has a literal obsession with hatred, it was his treasure. He could easily misinterpret 9S love for 2B for hatred. Or use a stronger word. Also, N2 (and thus machine network) knew about 2B real designation and even taunted her with that.
Operator 6O: This incident might’ve been 9S’ work, you know.
Operator 6O: Maybe he really had decided to kill you.—Lies (2B/Pascal) 
But what about “destroy everything”?
9S is not an innocent boy and his №9 personality is well known to have psychotic tendencies when being triggered. That said, none of 9S selves as well as his latest one showed anything malicious towards 2B. Especially since Adam says how much 9S was thinking about it. It's important to mention that him being psychotic is definitely not part of his normal persona. Quite the opposite, he would often prefer to avoid combat and instead not fight if necessary (such as when it came to the initial meeting with A2, as well as the YoRHa deserters.) And while you could argue that his views towards machines is a reflection of his more murderous tendencies, that also doesn't add up as throughout Route A/B he begins to question the propaganda of machines being emotionless and incapable of feeling.
There is none. The word is intentionally hidden/censored. It is possible that it is not even 4-letters in English. You are free to choose whatever you please given all of the explanations above.
Related: Lore FAQ - 2B and 9S relationship