"She was alive when they ambulance left so..." - It should be "the ambulance."
"my boss started at me dumbfounded." - I think you mean "stared."
"I slowly wander back to my office" - It should be "wandered, past tense.
A general thing I would suggest is to not include so many ellipses. These punctuation marks should be used sparingly in creative writing. There were some times where they made me read the meanings of your words incorrectly.

Specifically: "Walking down a long constantly curving corridor, Lemmok and Pavicca nob as two different Alien races" - I didn't understand what "nob" means in this context. It brought me out of the story, trying to figure out its meaning.
More generally, you use the word "that" a number of times when "the" would have been more appropriate. For example, "Lemmok got up and escorted that female crewmember to the entrance into that small room." It would be better to say "the female crew member" and "the small room." Or, even better, to give them both a little description.

"He had a military bearing and stood straight, His eyes ..." - It should be a full stop after "straight," not a comma.

"'And DON'T try simply asking her,' Dad was saying." - I would say "Dad said." It is more active and less passive.
"Mom had carefully extracted one, two, three ... fortunes out of their respective cookies." - I'm not sure about the use of ellipses here. If you wanted to play on the word "fortunes" I would italicise it, and not use the ellipses.

"A second before Rachel Grant found herself standing alone on a cool, shady mountain side in an evergreen forest; she’d been ..." - This should be a comma, not a semi colon.
"A short hike up to the trail’s crest, presented Rachel ..." - The comma isn't needed here.
"The amphitheater appeared to have exits like the Chicago Cub’s ballpark." - I could be wrong here, but I think the club is called Chicago Cubs, right? Not Chicago Cub? Assuming it is, the apostrophe should be after the s.
"Rachel interrupted him, 'who’s we?'” - It should be a capital W here at the start of the dialogue.
"Thank you for your incite." - It should be "insight" because "incite" means to call people to do something (usually riotous)

"Unconsciously peeling off her wetsuit ..." - I don't think unconsciously is the right word because the means literally being unconscious, which Serena isn't. Maybe, "distractedly" or "subconsciously" would work better?

" ...waves lost their energy and he would paddle out once more. " - I would put a comma after energy because, "and he would paddle out once more" is a separate clause.

Just watch your new paragraph spacing because you haven't double-spaced it in some places.

The last paragraph is all in italics, and I can't work out if you've done that on purpose, or if it is a mistake. I don't think it is an internal thought, so I can't see why it should be italics. But I'm open to being wrong.

In general, watch your use of semicolons. These should be used sparingly in fiction, and there are only certain circumstances where they are technically the right punctuation to use.
"'You might say, I may be overweight, but, this means that I have more love to give, I have expanded my horizons' Ha! Ha! I can choose to be a mare or a colt, but, whichever I choose, I have a mane and a tail; the mane guides me to the main pathway." - A couple of things here. You need to have some form of punctuation when you close speech marks. Secondly, I'm not sure why you have closed the speech marks, then continued with the speech but with no speech marks. You do this in a couple of places, and it makes the text a little bumpy to read.
"It was now time for Mrs. Whitmire's next project. She wants the class to be creative." - You have switched tense from past to present. I would just check the rest of the story for places where you have done this. It is easily fixed.
"'If people wouldn't be so angry at each other, then the temperature would cool down. Their anger was red hot ..." - Firstly, you haven't closed the speech marks after down. But, more importantly, who is they? It is uncelear to whom you are referring and, again, brings the reader out of the story.

"For a time she had seemed to read his mind translating what ..." - You need a comma after "mind" to show that it is Laura who is translating, and not his own mind (does that make sense?).
"When he had tried to speak it had come out wrong ..." - To make this sentence more active, take out the "had"s and change it to "came out wrong".
"Lavender" - This doesn't need to be capitalised.
" ...and removed it from the flower bed putting it in his pocket." - You need a comma after "bed" to show that it is Danny putting the weed in his pocket, not the flower bed. I know it is obvious, but grammatically, you need to show this.
"Danny thought to himself, yes that makes sense, that is how the word should be said. and he nodded." - The period here should be a comma.
"She's not remarried you know and is in a bad way." - I would put commas either side of "you know"
"The buttons were bigger here than on the old laptop or the phone and he could type" - You need a comma before "and."
"Are you two back together, Oh praise God!" - It should be a period instead of a comma after "together." Also, I would place a comma after "Oh." Or, even, an exclamation mark would work.
"Sounds like a plan and will you?" - You need a comma after "plan."
"Already done it Pastor and ..." - You need commas either side of "Pastor" because Danny is addressing him directly.