Ever since when Jack left the Autobot base and hadn't been seen in weeks,  everyone was worried about him. Hell, even Arcee was concerned that something had happened to him. Then, they also heard that a new group would help the Autobots, and this new task force was called N.E.S.T.

Miko: So you guys are getting a new army to fight the cons!! Awesome!!

Raf: Do you think they know what they are getting into?

Optimus: I am sure their government told them what they are getting into.

Ratchet: Optimus agent Fowler is here with one of the soldiers who will help us.

Optimus: let them in.

When Optimus said that Agent Fowler, along with a man in armor 

Fowler: everyone, I want you to meet CC-2225

(Jack uses his number, so they don't know it's him.)

Jack: When Agent Fowler asked me if my army could join your war, I had my reason not to, but that doesn't matter. Whatever you are from, you got it. The clone army is under your command.

Raf: clone army? 

Jack: yes, 

Fowler: The clone army is a military project we keep secret.

Rachet: so your government was making a new army. Why?

Fowler: (lied) When you came to earth, we wanted to create an army in case you lost and would leave us defenseless, so our government made the clone army.

Ratchet: So you've been making this army for the last three years?

Fowler: longer.

Then Jack gets a call from Lock.

Jack: sir, I got word from Lock that they are ready for the assault.

Fowler: How did you find him?

Jack: you don't want to know.

Optimus: before you leave, what is your real name?

Jack: Sorry, that is the classified agent. We can watch Base 407 do the mission.

 (start at 2:42 to 4:33 also replace insurgent as mech)

https://youtu.be/g-H9TVRX2Ic

Jack: And is it how we do it?

Fowler: yeah, but...

Jack: no.no.no. We got our guy, and one died.

Bulkhead: no one died?!?!

Miko: but that was awesome!!

Jack: you think this is some sick game?!

Everyone looked at him.

Jack: Yeah, I know they were ruthless when they breached because that is how we were trained to kill the threat, and after every mission, my brothers and I have to live with the fact of what we did...

Miko: yeah, I can't be that bad.

Jack: listen here, you little brat. I lost so many of my brothers over the years, and many of them were my friends.

Then Jack leaves Fowler and follows him.

Arcee: battles leave scars, some you can't see. 

In the elevator.

Fowler: okay, what the hell was that about?!

Jack: what?

Fowler: What you said to Miko!! I know she goes through the ground bridge to see the bots in action, but that doesn't mean you have to grill her like that.

Jack: Someone has too because if she does what she does, she can get Raf or anyone killed because  of stupid stunts

As Jack walked to the gunship, Shepard came to give him the reports.

Shepard: General Lock reported that there is a con there.

Jack: what's their name?

Shepard:  Arachnid, sir, and by the looks of it, she was a test subject for their experiments. 

Jack: Is she okay?

Shepard: Yes, sir, we got her in the transport, and she is at base alpha.

Jack: Good, we can get information on Megatron and the Decepticons.

Shepard: excellent, sir...

Jack: is there a problem commander?

Shepard: nothing, sir.

Jack: Speak up, shepherd

Shepard: Sir, we all agree to join the fight, but...

Jack: but what?

Shepard: what happens when we win this war, and what happens to us?

Jack: we will live as free men.  Let's head back to base.

as they went back to base, they saw clones running to hanger 12

Jack: trooper, what is happening?

 Boil: the prisoners are causing problems. Sir Fox is calling for backup,

 then Jack and Shepard run off to the hanger to see  what is going on

Fox: listen here, lady. My men will be forced to put you down if you don't calm down.

Arachnid: tell me why I am here. Are you with mech?

Fox: no, we are not. We are with the US government and their allies, including the Autobots.

Arachnid: You don't look much, and your weapons are more advanced than theirs.

Jack: arachnid, stand down.

Arachnid: sorry, I won't. How do I know that you won't lie to me?

Then Jack did something that no one would think he would do.

Arachnid: Jack?!?

Jack: yeah, it's me.

Arachnid: but how?

Jack: I was a clone of the Grand Army Republic and the Galactic Empire. Now, I lead the clone army that went rogue when I discovered the truth about the empire.

Arachnid: what?

Jack: it's a long story, but let my men help you for now.

Arachnid: okay, I will, but can you stay with me?

Jack nodded and told the other clones to stand down. And they left the room, and Jack stayed with her. At the Autobot base, Arcee was in her room trying to call Jack.

Arcee: come on, Jack, pick up

But it went to voicemail.

Arcee: Hey Jack, it's been a while since we last talked or saw each other. I just wanted to make sure you are okay... so please call me back, or I will hunt you down.

Optimus: Arcee, I know you are worried about Jack, but we must give him time.

Arcee: how can I know if he is safe?

Optimus: Jack has shown from time to time that he is capable that he can handle himself 

Arcee: I know, but there is something about clones...

Optimus: what do you mean?

Arcee: he almost sounds like Jack... but I could be wrong 

Optimus: You may be correct, but I don't like how they operate.  

Arcee: Yeah, I only thought Mech would do what they would do that.

Optimus: get some rest, Arcee.

Then Optimus walks off, leaving Arcee and she wondering if Jack has anything to do with the clone army.