Some ideas I had.

New characters:

Vicky Viper - Name is a pun on Vic Viper. Pilot. Did you once say that you would be able to fly one of the ships through the MoonBase? She could give you missions to fly through goals.

Ross Well - Name is a pun on Roswell. Scientist; gives you missions to capture Grabbles for study.

Returning characters:

Jim Spaceborn - I only own the first book in the comic series, but here is what I know about Jim. Jim was the main character in a series of comics written by Frank Madsen and published by LEGO. In the first comic, Jim met up with a robot that became his sidekick, Keko. According to the first comic, he was found on an abandoned space ship when he was a baby by the Spearhead, a ship looking for new planets to explore. He was taken in by the crew, and has lived in space most of his life.

Keko - Jim's sidekick. Keko was part of a group of robots that lived on the planet Robus, until a villain named Kazak showed up and conquered Robus and many surrounding planets. Some of the robots escaped, others were captured. Keko stole a cruiser from Kazak and took off, but ran out of fuel and crash landed on a nearby planet called Commercia, a massive trading hub. Due to damage from the crash, he could not speak, and was taken into a junk shop, where Jim found and bought him. He was then fixed by Duncan, the Spearhead's head mechanic, where he told them about Kazak's invasion. With the help of Duncan and Jim, the remaining robots were able to defeat Kazak's army, though Kazak himself escaped.

One of the key parts of the first comic is a device called a Transformat, a little black camera-like device invented by Duncan that can strip down and re-build objects made out of bricks at high speeds. When Jim bought Keko, he gave the seller a Transformat, which was then taken by Kazak's henchmen. After figuring out how to use the Transformat to create other Transformats, Kazak planned to use them to quickly destroy the escaped robots. However, Duncan figured out how to protect the robots, and after installing "Anti-Transformats" into them, they were able to take down Kazak's troops. The Transformat rays were deflected back, and trapped the shooter inside a very strong force field bubble. So, what does this have to do with the MoonBase? One idea is that in order to trap the Grabbles for Ross Well, you would need a device which would be somewhat like a cross between a Transformat and an "Anti-Transformat", which would shoot like a Transformat, but trap the target in the bubble. In order to get this device, you would have to do some missions for Jim and Keko. No idea what those missions would be though... Anybody else got ideas for that?

To follow up on that: what if the Piratron also wanted you to capture Grabbles for study, and you had to decide which side you wanted to take the captured Grabbles to?

As for what missions you'd need to get the "bubble device": why not say that you must retrieve the three pieces of the device in order for Ross Well to build it for you? One piece would be locked in a secure Moonbase Alpha vault, and you'd have to complete missions for other characers in order to gain access. One piece was stolen by the Piratron, and you'd have to sneak into their territory to retrieve it. The last piece was aboard one of the Moonbase Alpha ships that was shot down, and you have to go out and smash smashables near the crash site to find it. Once you have all three pieces, Ross Well builds you the "bubble device" and asks you to capture 5 grabbles for him.