How does Zola end up like this in The Winter Soldier?

Question

I'm watching all the Marvel films through for the first time, and I've also never read the comics. I'm currently watching Captain America: The Winter Soldier and I'm not really sure I understand the whole "Dr Zola being alive in a computer" thing.

So Natasha, the Captain and Zola discuss how the US/SHIELD recruited Nazi and HYDRA scientists, and that Zola was dying so SHIELD somehow stored his brain in a computer so that he can still work for SHIELD etc.

But what I don't really understand is:

• After several decades, why is he still stored in ~70's era computer equipment? If he's that valuable to SHIELD, why didn't he ever get "upgraded"?
• Also, why is he still being kept in an abandoned military camp that SHIELD used to have an office in? Again, if he's valuable enough to transfer his brain to a computer, why would they then leave him gathering dust in a very deep basement?
• He's obviously still in communication with the elements of HYDRA within SHIELD, because he seems to be the mastermind behind the algorithm and the new helicarriers, and he knew that Nick Fury had been assassinated. So in that case, how is it that no one at SHIELD is really aware that Zola is "alive"? SHIELD were the ones to transfer his brain to the computer system, so why did they seem to forget about him? Zola alludes to having Howard Stark be killed in the past, but I'm sure Howard Stark wasn't the only person who knew of Zola being transferred to a computer.
• Zola is obviously determined to stay in existence, and yet at the same time also committed suicide by having SHIELD launch the missiles at the basement containing himself, Captain, and Natasha. Why would he do that to himself?

I'm sure this is probably more explained in the comics, but I've not read them.

Answer 1

All we really see is something that looks and sounds like Zola displayed on an old monitor for a few minutes.

As HYDRA's objective at the time was to distract them long enough for the missile to hit, it could all have been basically a puppet show to delay them. Everything shown could have been lies (except the algorithm obviously).

Zola might not even be dead.

Even if his mind is uploaded, it could easily have just been talking to them remotely.

Answer 2

Zola is a brilliant scientist and devoted dearly to Hydra. There is a reason why he didn't kill himself when he got caught, so basically he got a plan to resurrect Hydra from falling.

He created the Hydra algorithm for future targets. If Zola is still alive, for sure he'd have a better technology at hand - not 70s. So, to answer your question, these techs in the basement is being programmed by himself when he was alive - he programmed his self AI with a face identifying camera and all lots of datas. I bet SHIELD doesn't dare to "upgrade" him because they might accidentally did something else that could potentially shut him down.

Hydra has become evolved and even the senator was a part of it. The secret agencies including SHIELD gave data to Zola's AI of all the people in the world, their records. This make it easier for Zola's AI to identify Cap and Black Widow, called in their whereabouts to SHIELD and stall them for some time.

You don't put a valuable asset in a plain sight. It was hidden in SHIELD's old secret office because SHIELD don't want it to be found. No one can suspect SHIELD as their aim is to bring Hydra down. They think no one will find it if it's left in an old Base Camp. Well, I think you'd have done the same.

There's only a limited number of people that know about Zola as he mentioned and obviously he tries recruited all of the powerful ones or those who aren't a threat to Hydra as the algorithm is; the Undersecretary and Senator are recruited. But he wouldn't just approach a harmless (according to Hydra) normal person as well. Zola might create another algorithm that can find future Hydra's members as well, if he can make the one to identify threats.

So, it's plausible that Zola approached Howard Stark to join Hydra because Howard's records shows he's the man who'd like to go big, high tech, playboy (to Zola, Howard cares about power). But of course Howard is a good guy, rejected him, and Zola assassinated him. As Zola said, he's just one of the many who knows about this and got killed. Nick Fury is ordered to be directly assassinated because he has suspicion on SHIELD and Project Insight. The same goes for Cap.

As to the final question, after trying to understand why Zola would risk his "brain" is firstly, it's an AI of Zola, which he wouldn't mind being risked because as long as Cap and Black Widow is dead, at least no one can stop his Project Insight. For Zola, Hydra is more important than his "brain". As you know, Black Widow extracted the algorithm in the ship and I bet it's there in SHIELD too, accessible only to those with higher clearance, like Pierce, who was a Hydra member. So as long as the algorithm lives, they'll assassinate those threats with Insight helicarriers and "Hail Hydra".