In this episode it is said the the monkeys simply woke up in the Robot one day with no recollection of where it came from. But in the flashback during Secret of the Sixth Monkey it shows them standing around the Robot with Mandarin
One of the robots that Professor Maezono sends after the Hyperforce is the same one the Super Robot Frog team had in "Brothers in Arms" except it was a different color. This may mean they are also connected to Maezono, and possibly, the Alchemist.
Chiro: (to Prometheus Five) You know, you and the Super Robot make a great team.
Prometheus Five: My prototype has a message for you.
Chiro: What is it?
Prometheus Five: He says that he's already part of a great team.
Prometheus Five: (to Dr. Maezono) My prototype wants answers, and so do I! You helped create us! Dr. Takeuchi was supposed to be your friend! We were your legacy, and you've destroyed it all! Well, now it's time for the big payback, Professor!
Dr. Maezono: Not so fast, "son"... (flies away) I might be too quick for you!
Prometheus Five: (sends an energy blast at Maezono, but the Super Robot stops it and Maezono escapes) No! He deserved it! You should've let me destroy him!
Gibson: (after saving Sprx from one of Maezono's robots) As you would say, Sprx...I've got your back!
Sprx-77: (annoyed) Hmmph...thanks...
Prometheus Five: (to Chiro, about Dr. Maezono) Let's see...were you talking to a human being with a face? Or a disgusting heap of human brain on a plate?
Otto: It was a brain heap, for sure.
Prometheus Five: (to monkeys) I tried to establish a connection with you, but it didn't work. You robot monekys are just so...basic.
Antauri: (to Dr. Maezono) You say you are...one of the creators?
Dr. Maezono: Yes. Three brilliant minds worked together to create the ultimate fighting robot. The Super Robot was our first success. Or at least it would've benn...if you hadn't stolen it!
Sprx-77: Stolen?! Wait a micron! We didn't take him!
Chiro: I found the Super Robot abandoned on Shuggazoom, okay?
Otto: Yeah, we just woke up in him!
Dr. Maezono: (about the Super Robot) The prototype...is has returned!
Chiro: You mean you know ehere the Super Robot came from?
Mr. Maezono: Indeed. It came from here, in this very laboratory...and I was one of its creators.
Dr. Maezono: (looking through optic sensors) Robotic monkeys? I can scarely believe my optic interface!
Gibson: I concur!
(The Super Robot saves the Prometheus Five and it flies away)
Nova: (annoyed) You're welcome...
Otto: (about seeing the other similar-looking robot) It's like looking into a mirror...
Sprx-77: Yeah...a creepy, freaky funhouse mirror!
The third unnamed scientist is obvisouly the Alchemist who created the monkeys. This explains why the Robot disappeared when he did, and why the monkeys woke up inside of the Robot.
Scott Menville, who was the voice of Prometheus Five, also does the voice of Robin in Teen Titans, which is another show that Greg Cipes stars in as Beast Boy. This meant that two voice actors from Teen Titans appeared in this episode.
The Prometheus Five wants revenge on Dr. Maezono for Dr. Takeuchi's death, and goes after Maezono when he escapes.
Apparently, the monkeys know nothing about how they acquired the Super Robot. They claim to have just been awoken inside of it with no idea of how it got there.
According to the Prometheus Five, the Super Robot knows all about the Hyperforce, where it came from, and what has happened. Apparently, it is also very much content with being a part of the Monkey Team.
The Super Robot and all of its other models were created by three scientists, Dr. Maezono, Dr. Takeuchi, and an unnamed third scientist. Dr. Maezono attempted to use the Prometheus Five for his own unknown purposes, though he was stopped by Dr. Takeuchi. Unfortunately, Takeuchi was sacrificed in the process.
Chiro nicknames the Prometheus Five "Slingshot" for his ability to launch himself at his targets by creating slingshot-like projections of energy from his hands.
The Super Robot is the prototype of the Prometheus project. The most recent is the Prometheus Five.