And though neither of them knew it at the time, they had just ensured that the plans of basically every single person in the conflict to come were going to go completely wrong. Except Rin. Her plans went wrong just fine without any outside help.
In Chapter 5, Berserker has made short work of Rider and is prepared to do the same to Rin. Shirou won't have this and leaps in front, fully expecting to get skewered. And then Berserker... stops his descending sword, picks up Shirou "with the air of a gorilla lifting a kitten", and gently deposits him to the side. Everyone falls silent in shock (yes, even Shinji)... Then Berserker resumes his assigned task.
In Chapter 6, we get to the customary "Shirou asks Saber to train him scene", where he promises to be her best pupil ever:
Shirou (smiling widely): "Bring it on, sensei. I can take whatever you can dish out!" -Four Hours Later- Shirou is bruised, sweating and gasping for breath. Saber: "Would you liked to continue?" Shirou: "... maybe... we... should... stop... for... lunch." Saber: "That would be acceptable, yes."
Chapter 7, after Shirou arrives home 5 hours late to face Saber and Taiga:
Shirou stood before the Judges of Hell, and knew that he was amongst the damned.
Watching Shinji getting battered in various ways through Chapters 3-5.
Especially when Archer does it to Rin a second time:
"I can run! Just set me down and AAAAAAAAAAAAAAAAAAAAAAH!" Rin said, as Archer threw her. He was much stronger than a normal person, and he didn't need much more than a fairly low-key motion of his muscles to manage it. In his defense, though, he didn't throw her into a bush again. It was a pond.