I just want to say that the System Alliance is not recognised by the UEG/UNSC, so the Alliance is not much different than the Insurrectionist who consorted with the Covenant. (Take note of the Rubble incident)

And ONI does work with rebels/terrorist in the book series Glasslands (takes place between Halo3 (the Bungie Halo) and halo4 (the 343 halo , the people who ruined the halo franchise with halo5)), ONI is actively funding an anti-human Sangheili against the arbiter who was the pro-human group.

On the surface the UNSC sang praises to the Arbiter but behind the scenes ONI is actively trying to undermine the Arbiter.

ONI did this to because ONI doesn't trust in words. What ONI wants is actually facts, they want the Sangheili to not have the capabilities to go against humanity even if they wanted to.

So they started supplying an anti-human Sangheili group and eventually caused a civil war amongst the Sangheili further weakening them, ONI wins in the end as they achieves their original objectives.

ONI again is doing the dirty jobs that no one is willing to do.

Now that is settled, the Spartan project falls under ONI, so do you think an ONI trained Spartan would mind doing dirty jobs against aliens for the advancement of the human cause?

Also I do think the Insurrectionist views the Spartans as the terrorist in some of the books I've read and if I remember correctly the Master Chief nearly blows a hole at an Insurrectionist space habitat almost killing everyone in it.

There's also the case with Gray team with the Rubble too, if you ask me they should have blown the place sky high with the nuke for selling the coordinates of human colonies to the covenant.

-- story start--

After agreeing

B312 loaded his into crates and then carries them to the scheduled meeting place.

Crates?

Yes, it includes the hard plates for his MJOLNIR armor, his Spartan Laser, his M6 pistol, a bunch equipments, his unfinished slipspace drive and a few other bits and bobs that's not worth mentioning.

He places his crates of luggages at the landing and waited for his pick up.

Moments later a shuttle arrives and lands right in front of him.

The hatch opens revealing the supposedly dead hero Shepard, the Cerberus agent Lawson and the Quarian what's it face.

"Wow, I didn't expect to one we've been searched for to be this big" exclaims the supposed dead hero.

"I just hope he is as good as he looks to be, especially the amount Cerberus is paying him" the Cerberus operative said while raising an eyebrow at his height and build.

"Shepard, I didn't know Humans grow the big" saids the rat bag.

"They usually don't" the red head replies

"As agreed upon I will now be joining you" B312 saids as he start dragging his crates of luggage aboard the shuttle.

Donk

A loud thud range out through the hall of the shuttle as the Spartan places the crate into the shuttle's hold.

"What's inside the crates? They sound heavy" the red head asked curiously

"Personal effects" B312 replied not saying more on the matter and walks pass Shepard and the crew to fetch the other crates.

"Well... at least he seems the part" Shepard said as she stares at the 2 meter tall Mercenary easily pulls up another heavy crate into the shuttle's hold.

Later Aboard the Normandy

The Spartan eventually got aquatinted with the crew and eventually got his own personal quarters at the ship's Cargo bay (zaeed won't be making an appearance in this novel).

Once he arrives at his quarters the first thing he did is naturally is to look for surveillance devices and disable them when found.

Of course the ship's AI naturally protested at his actions of damaging the surveillance cameras, suffice to say it didn't take long for Shepard to come and ask him what he was doing damaging the ship.

"What do you think you're doing damaging the ship!" She asked seemingly quite grumpy as she came as soon as she heard from EDI that the giant mercenary is vandalising the ship.

To which the ONI Spartan just simply replies "Privacy" as he crushed a surveillance camera in his hand before continuing "I've only removed the surveillance cameras within this room"

She stares at him for a bit before eventually just sighs and said " just don't damaging anymore of the ship"

"Understood" he replies.

With that Shepard walks out of the cargo area.

With Shepard gone and all the bugs cleared the Spartan then began unpacking, he began setting up the various equipment within the crates that are crucial in making a slipspace drive.