The car scene also plays out. "we were supposed to be allies" is a reference to Tyrell offering Elliot a job. The "I know your dirty little secret" is a reference to Tyrell being aware that Elliot set Colby up.

I think Tyrell will force Elliot to stop it, so he can go back to Evil Corp and say: "Look!! I saved the company!!!"

This scene didn't bother me at all. When Darlene said "please tell me it's ok to execute" I saw it more as a final, beaten down plea. Elliot (as Mr Robot) had just blown up, but she weathered it, and was asking one final time…Please.

The reason Tyrell said "We were supposed to be allies" to Mr Robot is because he sees Elliot, and he tried to recruit Elliot.