OK, guys, this is my first try at making a theory so bear with me. Before I get started, many thanks to Great Being (or is it Bisc and Toa now?) and his “Before-Time” topic. That influenced most of this theory.

I remember hearing some people thought that the Bohrok were created by Makuta in case he was defeated. After reading the above mentioned topic and seeing that Makuta released them early, I got to thinking. What if the Bohrok were created by Mata-Nui? Perhaps, as he began to notice Makuta’s growing darkness, he designed the Bohrok to be a clean-up crew to return Mata-Nui(the island) to its original conditions in case it was devastated by a conflict between Mata-Nui and his brother.
-The Bahrag's mission was to turn Mata-Nui into the way it was in the "Before Time". GregF
The Krana might have been designed as master switches for the Bohrok so that if one malfunctioned, its Bohrok could be captured, have its Krana removed and replaced, and sent back to work. This way the malfunctioning krana would not force them to scrap the entire Bohrok because one part broke. The Bahrag were designed to act as command and control units for the krana. Thus the krana were not independent and could not “revolt”. The krana were also useless if the Bahrag were captured. This way, if for some reason the Bahrag malfunctioned, the Swarm could be shut down taking out the main controllers. Makuta saw his brother’s invention and subtly began to corrupt the Bahrag as they were the only thing that controlled the Bohrok. He did this to spite his brother. As the Bahrag began to be influenced by Makuta, they upped the power of the Krana so that they could control anything they wanted and not just the weak-minded machine Bohrok. In this they subconsciously were imitating Makuta’s infected masks because of his influence. Makuta’s manipulation also created a fanatical sense of purpose in the Bahrag. They would accomplish their mission, no matter what ,or who, stood in their way. They wouldn’t even allow the changing decisions of their creator to stand in their way. They were unaware of Makuta’s tampering however. Mata-Nui became aware of the tampering, though. He sadly sealed away his creations in the depths of Mangaia. Since no one lived upon the island at that point, the swarms would be safe there until Mata-Nui could figure out how to repair the damage. When Makuta came to power, he purposely built his lair by the Bohrok and Bahrag’s location so that he could awaken them when he wanted.
- From GregF:Well, the Bahrag didn't seem to think there was anything on the surface that could interfere with their job.. which would seem to imply they didn't know there were Matoran villages on the island. Maybe there shouldn't have been at the time the Bohrok were released... maybe the Bohrok were not supposed to be released as long as there was anything alive on the island (after all, they never tried to harm the Matoran, or even noticed them much). But when they were released by Makuta, they became a threat, because there were villagers and homes on the island that were put in danger by the swarms.When they were awakened by Makuta, the Bahrag assumed that it was time to fulfill their mission and began to awaken the swarms and assign them tasks. When they called the Toa their “brothers”, they were referring to the fact that they recognized that the Toa shared a mutual “parent” in Mata-Nui. They realized this through the Toa’s use of the same elemental powers that they had been endowed with by Mata-Nui. They attacked the Toa so viciously not only because they were interfering with the mission but also because they were enraged that their “brothers” would oppose them when they were only doing what they were told to do. They would assume that the Toa knew about their mission and were getting in the way on purpose. Thus, Makuta’s plan was to simply release them early so that their natural mission would destroy anything that got in the way, as he was sure that the Toa would as they would try to defend the Matoran. This would also give him time to regenerate his strength and create the Rahkshi. Also, since the Protodermis well was nearby but inaccessible to him, he would let the Toa open it for him. The Protodermis was put there to transform the Toa so that they would be ready to take on whatever threat to the island was powerful enough to release the Bohrok early. Makuta needed it to create his Rahkshi. If the Toa opened the well, Makuta would be able to create his most powerful minions ever and also give the Toa Nuva a devastating weakness: the Nuva symbols. He knew that these symbols could disable the powers of the TN. What he didn’t count on was that the Matoran would be able to wake Taka Nuva.

Intersesting...so Makuta knew the toa would beat the bohrok? Planned on it infact? Well that leaves out the Bohrok Kal.

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This would also give him time to regenerate his strength and create the Rahkshi.

Why would Makuta want the Kal to re-awaken the Bahrag if they served only as a distraction for the toa so he could prepare the rahkshi? sorry if this makes no sense to you.

Polo, I think that the bahrag AKA bohrok, were good, but under influence of Makuta, did bad. The bohrok-kal were probably just trying to do good and release their masters and live freely.

The BK would probably be part of the original plan incorporated by Mata-Nui if Makuta defeated the Bahrag.