4

Mike was injured, and Gus was unconscious. It was a perfect chance to kill them both. I thought Jesse wanted to kill Gus, so why he didn't do it then?

5

Jesse was not a killer by nature. He was forced to kill Gale, but it tortured him, and he never voluntarily took a life.

Until Todd, of course.

1

Your premise is flawed, Jesse does not want to kill Gus, at least not at that point in the show.

Walt wanted to kill Gus ever since the season 4 opener, Box Cutter, as he believed Gus would kill them the first chance he got. However, Jesse was not as easy to convince. While Walt was trying to convince Jesse that they needed to kill Gus, Gus and Mike were doing everything they could to get Jesse on their side against Walt.

Even though Jesse tells Walt in "Problem Dog" that he will kill Gus the first chance he gets; we also see Jesse lying to Walt about having met with Gus in person since the events of Box Cutter. Jesse is very unsure about where his own loyalties are at this point; torn between the two sides. But he certainly isn't desiring to kill Gus.

It is not until Walt tricks Jesse into thinking that Gus poisoned Brock in "End Times" that Jesse is finally convinced that he should help kill Gus. Up until then, he was being successfully manipulated by Gus and Mike into being a part of their "team".

This, in addition to the other answer, which explains that Jesse in general was not someone who could easily murder anyone.

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