In a nutshell, it's a three-step process: warning, preservation, and disappearance.
Today, Hydra's organizational structure resembles a gigantic tree, with every primary branch related to countless smaller branches which in turn lead to multiple offshoots.
Their human resources structure is similar to a spindle - the majority of their staff are mid-level employees. Unlike the foot soldiers who work unknowingly for Hydra, these individuals have chosen to join Hydra because of its ideology. Yet they work not just for the ideal, but also for personal gains when necessary, much like the majority of spies in the world.
Within every organization, there is a proportion of individuals with flawed thinking. Due to the vast number of mid-level staff in Hydra, these individuals are particularly numerous, and most likely to slip up are the intellectuals Steve once mentioned.
They are not professional operatives or trained as such. Yet, because of their professional authority, they are highly esteemed. Many among them place self-interests first and are unwilling to make sacrifices to cover their own tracks. Hence, Steve and Stark have been able to unearth a chain of connections by—quite literally—uprooting these individuals from the ground.
Doctor Schiller managed to turn the tide by turning on this group. If it were to be summarised, it would be in four words that describe a drastic approach: pruning back deadwood.
All data must be destroyed, all experimental instruments damaged beyond repair during an evacuation, and even the headquarters can be burned down. Doctor Schiller will not contact the head of the base in this circumstance, who are usually PhDs or professors. Instead, he will contact security personnel and order them to forcibly remove the researchers. Anyone unwilling to comply is to be executed on the spot.
Doctor Schiller's reasoning is quite viable. Knowledge and data must be preserved, and there is no denying that the most valuable intellectual properties of Hydra are its researchers. Hence they are required to evacuate, and any disobedience is considered a relocation casualty.
In most research bases, tensions between security personnel and researchers are longstanding, since any professional operative would not be able to tolerate the assertive and intrusive nature of these scientists.
Therefore, after receiving orders from Doctor Schiller, the evacuation execution is done swiftly. There are no more procrastination, leaving the power on, or failed data destruction, nor will there be multiple boxes of hard drives left behind.
One might ask, if such a plan effectively combats Stark and Steve's investigations and attacks, then why didn't Hydra adopt it sooner?
From a bird's-eye view, one would find that the number of Hydra talents lost in the evacuations arranged by Doctor Schiller far outnumber those captured by Stark and Steve.
Kill your own, leaving the enemy with no one to kill—that's the secret to success.
Put simply, the ocean isn't Doctor Shiller's; he can sail wherever he pleases. He doesn't have to worry about how Hydra will handle the halts in experiments or the maintenance issues caused by the massive loss of technical personnel.
However, from another standpoint, Stark and Steve were caught off-guard. In the Avengers headquarters, Stark, his temples throbbing, said, "I think we need to reassess Hydra's leadership. They're actually willing to endure significant losses to ensure their escape."
Steve looked hesitant as he replied, "I suspect they might have received direct orders from the German headquarters."
"Back in my fighting days, it was common knowledge that Hydra in America was insignificant. Little Mustache's men were the ones to fear. Although I often refer to them as a bunch of lunatics, I have to admit, his key personnel are intimidating."
"Indeed, such decisive decisions aren't something ordinary people could make. They're far more formidable than I thought," Stark said with a grim expression. He then stood up from the couch and walked over to the tactical map, "My tactics against Hydra were adapted from those I had prepared against S.H.I.E.L.D., specifically against Nick Fury."
"But as we can see now, the adversaries are more ruthless than Nick. They were willing to lose two-thirds of the base just to ensure the safety of their key personnel while evacuating..."
"But we have to admit, they are smart," Steve stepped closer to Stark, standing beside him. "In fact, this is probably the best choice. Had they procrastinated and given thought to sacrifices from the start, they would've crumbled by now."
"Because the more important personnel we capture, the more branches along the main stem we uncover," Stark smoothly added. "Capturing a hundred branches does not compare to capturing just one primary stem."
"But it's strange..." Stark, furrowing his eyebrows, continued in confusion, "Initially, their response was withing my expectations. But recently, their strategical capabilities improved tremendously. If they had displayed this level of determination from the start, I would've had to reassess their threat level."
"That's why I say, there's a high chance that a formidable figure from the German headquarters has taken over. Such a style of operation is reminiscent of Red Skull's men."
"We need to reconstruct our battle plans. If necessary, I will seek help from the Luminous Alliance," Stark concluded, crossing his arms.
"First, let's arrange for an internal meeting within the Avengers," Steve suggested, walking over to the conference table he sat down. Just then, Stark's pocket rang out. He fished out his phone and answered, "Hello? Shiller?... Why is it you again, could you stop calling me?"
To Stark's surprise, the man on the other end hung up quite briskly. Shortly afterward, Peter, who had been playing billiards nearby, had his phone ringing. He picked up the call and answered, "Hello? Doctor Schiller?... What? How are our plans coming along? Not very well, Mr. Stark and Captain are considering readjusting the tactics..."
"Alright, I will nudge them for you, but why are you in such a hurry?"
"...Oh, indeed, this damned evil organization has hurt too many people and we indeed need to take immediate action to prevent them from causing more chaos!" Peter said, his face grave as he spoke into the phone, "Right! That's what I think too. I'm leaving now!"
After wrapping up the call, he walked over to Stark and Steve and relayed, "Doctor Schiller asked me to ask you why there has been no progress in the last few days? He is very anxious..."
Keeping his poker face, Peter conveyed, "He says he can no longer abide the evil of Hydra, not even for a second more!"