I went with the Nomad ending where you get Johnny erased from your memory with my Female V. "As my character would want that out of her head" I know there is other options where you can let johnny take over your body but you die or get trapped in the net. What if there was another option. You get johnny out of your head/body and you help johnny get a new body. Maybe a doner body and johnny gets a 2nd chance on life and can be a partner like Jackie and he can be with rogue. I'd like an ending like that.

A good suggestion, but Hellman makes it clear that it is too late to remove the chip. This he says during the interrogation in the mission "Life During Wartime". And I personally don't think he would lie about that, under the circumstances.

I have had the thought of a getting donor body myself (after having completed the game several times and know the outcomes and endings), but our ingame characters doesn't know what we know.

But yeah, after having grabbed Hanako in the "Play It Safe" mission, instead of proceeding with the Arasaka ending as it is, I wouldn't mind having the option of putting a gun to her head (fighting Takemura if need be) and demand she make some calls to get the chip out of V, or her journey ends the same way as Saburo if she is unable to help (which the Arasaka ending proves that she is).

Also, the Nomad ending was one of the most glitched missions I have done. "Defeat hostiles", the quest log said - and the only ones around was friendly Nomads...who were all firing either blindly or at each other, confusing the hell out of me.

I'll be doing the secret ending again on my current playthrough. Did it first on patch 1.03, but the game was still bugged AF back then.

I've personally questioned Hellman's motives from the get go. The circumstances are being tortured by V and Takemura, and his way of getting back at both characters are screwing both of them over. Hellman has information that (he knows) can't be obtained elsewhere, so he can tell you anything he wants and you would just have to take his word.

As it should be - Hellman rather proved his own untrustworthiness when he left Arasaka to snuggle up to Kang Tao.
But while his motives certainly are questionable, his character is being displayed as a coward who would say anything to save his own skin. And between V and Takemura, I'd argue they know enough to be able to tell when / if Hellman is lying.

How does he get back at V and Takemura though? I don't remember further references of Hellman past that mission.

That one I fully agree with. Hellman may not be lying, but he has no reason to tell the whole truth either.
And he rather insistently wants V to go back to Arasaka, as they are "the only ones who can help".

Would make sense that Hellman would want that, and be the one who brings in both the relic and the test subject, considering he has likely burned all bridges with Kang Tao due to V's actions in taking care of the AV.

With Takemura's involvement - which I'm sure Kang Tao will get wind of - Kang Tao will likely hold Arasaka responsible for bringing Hellman back.

And suddenly Hellman has 2 corporations after him. Not really helpful for a relaxed retirement, I'm sure. If he comes back to Arasaka, bringing V and the chip with him, I'm sure they can forgive...for a time. No arguments there. Since Alt was basically Johnny's "dump and re-do" input, and she's a digitized version of the real Alt, I wouldn't be surprised if the AI Alt still held some resentment towards Johnny.
Kinda like a "you didn't care about me before, why should I care about you now"-relationship moment. With V caught in the middle. No worries - this is a video game, not politics. Video game conspiracy theories are expected. And I find from personal experience the best theories comes when the brain is a bit more...unfiltered (as it tends to be when not fully awake). :)

If you think about it. The real Alt and the real Johnny are both dead. The computer system AI probably controls ALT and Johnny and it may not be really them talking to you but talking to you kinda like how Jackie did. I got to replay the game through a few more times to get story known more.

But you can see easter eggs of The Matrix and Metal Gear Solid events in the twist of this game. Even Kojima is in it. I even put somewhat easter eggs in my game from the MGS series. If looking for that Stealth game like MGS you can look up Half/Bryan. That is my game. It has a gameplay style of MGS and C&C for certain back lore story. I made it back in 98 and used different engines but with me working a normal job 6 days a week its kind of hard to even get any work done anymore.

Reloading a save at the end. Johnny doesn't want your body and actually tells you not to listen to ALT and to take your body back as he leaves with ALT past the blackwall.
After watching the ending giving the body to Johnny, During the gameplay you can tell he feels really bad and that he shouldn't be there as it should be the real V in the body he is in.

During the ending as Johnny. He says I won't be a girl for long to the kid "Can't remember his name" but I am thinking that Johnny maybe taking the bus to find a way to rescue V and get her back into her body and end all that was done by arasaka.

But I think I will stay with the All Along the Watchtower "Star" ending for my character and probably the only real good ending in the game and probably the canon ending.

I think V doesn't die at the end and ALT just wants you to stay in the cyberspace and tells you only have 6 months to live to get you to think and stay.