Ako-Metru (Guard property) and the Field of Light!

That design is used.

They are given Staffs with the six powers. "What else should they do?"

Xia asks who the Captain of the Guard is.

"Sanok targeting scopes?"

"Done."

The designs are... uploaded?

Those regeneration tanks are hooked up to matoran armor.

Prototype Metru seeds are created.

After further examination, they discover that they can reprogram the protodites to perform tasks other then soothing a crowd. 

Unauthorized teleportation proof shields are made, and the frequencies are given to NA and Xia.

The Metru seeds are taken by Guard members to plant elsewhere.

With the right coding, protodites can be made to form anything in the known universe, such as 3D printers, kanoka, and even warriors! Guardsmen are taken in and analyzed for potential replication.

FAILURE!
   A mishap with the viruses sends the protodites into a frenzy, swarming around in their little glass box like the world was about to end.
   "Is that supposed to happen?" A concerned Ko-matoran Guardsman questions the nearest scientist, who is currently monitoring his vitals.
   The Vo-matoran scientist shifts her focus for a second to see what the Ko-matoran was referring to, then locks eyes with the Bo-Turaga frantically trying to calm the protodites down with sleep gases and even the occasional lullaby. "What did you do?" She asks, afraid of having to eliminate their project and go back to square one.
   "Nothing!" D'rin shouts. "I just gave them their daily rations! I didn't know they were this hungry!"
   A De-matoran bounds over to the monitor. "Uh, guys? It's working. They are bonding together like the molecules of a kanoka."
   "Really?" The Vo-matoran leaves the Guardsman and takes a look. "...but, they're so violent."
   "Why isn't the sleep gas working?  They should be knocked out by now."
   "Remove poison?" The Guardsman suggests. "You grabbed the sleep vial from a shelf that said, 'poisons.'"
   "He's right." The matoran of lightning states. "If that's the kanoka they're forming, then the gas won't do anything. I didn't think they had-."
   The box freezes.
   "I thought they were emulating a code four disk?" D'rin ponders.
   "They're like soldiers who were given new weapons." The Guardsman says. "Without a superior to order them around, they will find their own way. Right now they're just trying out their new powers."
   Half of the protodites teleport outside the box.
   The Vo-matoran scientist quickly locks the room under a Hau quarantine.

A Toa of Light observes the location

   "We can't do that from in here." The De-matoran responds. "But I bet you can."
   The turaga grows a wall of bark around the rahi, although it is clear that it won't hold them for long.
   The Guardsman positions himself between the swarm and the scientists, Crast shield equiped. "Can you make a quaruntine within a quaruntine or something? Because I'm not seeing a Hau disk in here."
   The De-matoran swipes the basic kanoka alloy off of the table and grabs a plasma torch. "I'm on it." He begins heating up the unpowered disk.
   "Uh... hurry!" The Ko-matoran demands, noticing a hole in the bark.
   "Just a second!" Parts of the raw kanoka metal become white hot. "There, I've activated it's Enlarge and Regenerate elements. It just needs to cool."
   The protodites rush the matoran, testing out their Weaken powers. The shield bounces them back, but doubles their number.
   "There!" The De-matoran takes the scalding hot Hau kanoka and holds within everyone's reach. "Strike it as hard as you can!"
   All three scientists, being behind the Ko-matoran, strike the kanoka, but before the Guardsman is able to do the same, is is overwhelmed by an entire swarm of RaR protodites.
   "Terau!" Screams the Vo-matoran.