In the ending of episode 2 Agent DiPierro realizes that Elliot knew he was being spied on, and sent a message to them. How?

You can actually visit the link in the email that he sent: https://sandbox.vflsruxm.net/plans.rar

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When decoded, we can see that this is actually a .rar file.

So, we can decode the base64, write it to a file, then unzip the file.

We get a .png file with a QR code.

When scanning the QR code, we get a link to this github: https://github.com/RedBalloonShenanigans/MonitorDarkly

It’s the exploit that they used on Elliot’s monitor!
Once Darlene left, Elliot loaded up Kali Linux and checked for RATs (Remote Access Tools) installed on his machine. This didn’t find anything, because the FBI actually attacked the firmware on his monitor instead of his computer. This allowed them to see what he was doing while simultaneously remaining undetected - or so they thought.

Elliot figured out that they had used an exploit on his monitor. So, he devised this clever email. When DiPerro says “it’s for us,” she had just deciphered the email link and realized that Elliot knew about their monitor exploit.