Hi there,
just started writing the 3rd act on one of my latest scripts, but I think that my 'twist' is not working properly. Question lies at the end..

This is pretty much how the script goes.
-Mikayla is a college soccer player, her dream is to go pro. Not only she has everything needed to achieve her goal (talent and such), but she will also do everything to get there. She's also arrogant, with a huge ego.
-During a training session, she gets injured (concussion and a nasty fall to the ground). It doesn't look like a serious injury, but she gets to the hospital nevertheless.
-Now, what we have here is two different timelines/2 parallel stories.
1. she wakes up at the hospital with a broken leg. Initially, all her dreams come to an end, after the doctors tell her that she won't be able to get back to her former status.
2. she wakes up on a bed, in restraints (in some cabin on a mountain far away from civilization), in full health, last thing she remembers is the injury she had, where Helen tells her a story (at the end the story proves to be fake) which goes like this; something happened and two parallel universes occur with Mikayla's life being the only difference among them.
- We move on
1. the injured Mikayla will do everything to heal her wounds and come back
2. Helen will persuade Mikayla to find her alter ego, kill her, take her place and achieve her dream because her 'other self' will not be able to ever manage this due to her injury.
The actual story relies on the Mandela effect, where the two Mikaylas have different memories of what happened... until they finally meet.

Now, what happened and there are two Mikaylas?
Who is Helen and why does she need Mikayla to kill her alter ego?

Let's add some 'scientific crap' in here.
Long story short, the Cern experiment. Helen is the alter ego of a scientist there who tries to make one of the Cern projects fail, because she's afraid of its results, such as the creation of parallel universes/timelines. Although she believes that the experiment was a success some time ago, because there are already two Helens already (her memories end up to the time of that experiment), she cannot kill her alter ego because she believes the latter is there to create problems to the machine, but she can undo the whole thing by killing the 'injured' Mikayla, thus 'killing' one of the timelines completely by doing this.

The injured Mikayla works hard to come back to full health, and she almost succeeds, she is ready to return.
The other Mikayla , convinced by Helen that she will fail (to go pro.. etc) due to the injury of her other self, she gets back to kill her, and take her place.

- the story has one or two more incidents occurring, but the question is this.

Why Helen doesn't go on a Mikayla hunt and kill her on her own? I need to find a reason she can't do it, because that 'won't work' properly in her plan. Any ideas?

First I will say the whole college soccer stuff has literally no bearing on the rest of the story, from the information you've provided.

Second, I think you should look more into the time-travel stuff. You have to come up with at least some PLAUSIBLE theory as to why there would be a clone (I assume you meant this rather than alter-ego) and how the timelines would be altered if you remove one of them from existence. Basically just watch some movies with alternate timelines and clones, like Primer. Since time-travel is fiction, there's no real research you can do, but Primer is probably one of the better examples on how to pull this off while still remaining "realistic."

Lastly, just share what you've written in the "Work in Progress" forum as this doesn't really accomplish anything.

Had me confused.  Sorry