Other than the comma and apostrophe problems, you also had a few other typos.

Do I make myself clear.

This should end in a question mark

Wait until we can rub this is Science Lad’s face!”

Is should be in

“My whereabouts however does not explain what you were doing on the ceiling of Sasha’s bedroom.

does should be do, I think.

As she finished the sentence she suddenly burst into the song, going through the opening bars of ‘Goldfinger’.

Goldfinger should be a better Bond song. I believe you meant 'Live and Let Die'

As for the Interlude itself...

I liked it. It wasn't terribly exciting or anything, or even funnier than an average interlude, let's say, but other than the grammar issues (big 'other than' there, you should really work on those) it seemed fine. The new trainees seem like an interesting bunch. Also...

Biggins nodded. “Thus speaks someone who has never been a field agent,” he replied. “It may be that putting them in the field is the worst punishment the Flowers could think of.”

That's exactly what I was thinking...

These pieces were both very enjoyable! I like the mixture of mission and PPC-goings on that you have happening here. You did some creative things in the mission that set it apart, and I also like the setup of strangeness happening in RC 4095. It has me intrigued! I wonder if the SO assigned them there so that any further incidents don't go unreported?

However, I also have to say that you need to work on your commas and apostrophes. As much as I enjoyed these stories, every time I hit a possessive with no apostrophe, it through right out of my train of thought. There were also quite a few misspelled words in the first one, such as "eventual looser" instead of "loser." I strongly suggest reading through them again with an eye for spelling and punctuation.

It's crazy to see that the Avengers movie is getting incredibly bad canon-breakers like this before the movie is even out. What the heck is up with that?

Anyway, this was a really fun mission. It was great to see the theory they came up with for finding the Sue without an RA. I also really liked how it took a non-standard format for the mission, and especially seeing the stuff the fic did to the continuum.

The canon split was really weird, but I'd love to see more of that.

So in other words, it's great that you're back to writing missions! :D

Forgot to mention in the first post, two mini's were pulled out of the mission.

SHIELD - A mini Samuel L Jackson style Nick Fury
SHEILD - A mini David Hasselhoff style Nick Fury

Both mini's will be appearing in future stories.