[HIGHLIGHT]SPOILER ALERT, I RUIN EVEN MORE OF THE STORY THAN Dil999 DID[/code]
A lot of those theories are completely ridiculous. Also, no offense, but learn to read books, you n00b. You learn Master Chief Petty Officer John SPARTAN 117's name in the first book (Halo: The Fall of Reach). He's not an alien, he's an above-average human that's been trained in all areas potentially useful to combat roles (tactics, weapons, piloting) since the age of five. He was specially selected with 74 (73?) other children of 150 potential "applicants" that were genetically screened for performance in the SPARTAN-II program. The first few bits of stuff that Cortana tells you (during the missions) in Halo 3 is what Catherine Halsey tells the "recruits" after they wake up from cryosleep and begin training. Of the 75 (74?) SPARTAN-IIs that underwent the physical augmentation surgery (lots and lots of surgery), approximately 35 survived and were in a condition to be of use in combat (maybe 34 or 33). Of those remaining SPARTAN-IIs, one died during the retrieval of the MJOLNIR MK.V armour systems, which further increased the SPARTANs' incredible combat abilities (lol, made them as strong as a Covenant Elite all on its own).
He steps out of the cryosleep chamber in the first one on a Halcyon-class ship known as the Pillar of Autumn... He's on another ship known as the In Amber Clad in Halo 3. The original reason he was on the Pillar of Autumn in Halo: Combat Evolved was to infiltrate and commandeer a Covenant flagship, with the ultimate goal of capturing a prophet and negotiating a truce between Earth and her colonies and the Covenant.
Unfortunately, during the previous encounter with the Covenant (which I believe occurred over the planet that John 117 was born on), a tracker is landed on the ship of one Commander Jacob Keyes, who ironically was just promoted. Interestingly, as a lieutenant, Keyes had escorted Catherine Halsey (the scientist in charge of the SPARTAN-II project) to conduct reconnaisance on an undisclosed (although most likely large) amount of potential SPARTAN-IIs.
Captain Keyes unknowingly lead the Covenant straight to Reach, the humans' main shipyard and military base. So, as the Pillar of Autumn was leaving Reach for Covenant space, they received a distress call and went back with the rest of the fleet. Every SPARTAN-II that could be called to Reach was; I believe that only two were not taking part in the mission to take a prophet hostage.
Approximately 30 SPARTANs went down to the surface of Reach to fight off the Covenant invasion force (and receive newer stuff, lol) while 3 SPARTANs went to destroy a navigation database that the Covenant could have potentially used to locate Earth. The pelican that the 30 SPARTANs took groundside was shot down, and approximately 4 or 5 of them survived. Overall, two SPARTAN-IIs were onboard the Pillar of Autumn when Cortana entered slipstream space to escape. One of those SPARTAN-IIs was John 117, and the other was Linda 058, who was more or less clinically dead.
Cortana's "randomized" coordinates were taken from data gathered during the previous fight, which got Captain Keyes promoted and his ship tracked. Thus, Halo (Installation 04) is discovered. The Covenant were not only already there, but had chased the Pillar of Autumn. Captain Keyes woke John 117 in anticipation of being boarded, and Halo begins. On a side-note, the Master Chief picks up Johnson, several other marines, and Linda 058's cryosleep tube on his way back to Earth. And that's the beginning of Halo: First Strike.
If you're too lazy to read all of that, Dil999 needs to read more.
Anyways, the planet is probably Onyx, where the surviving SPARTAN-IIs (with the exception of the two that were too far to be recalled for the Pillar of Autumn mission) and Dr. Catherine Halsey should be. Onyx is more or less an artificial planet made by the forerunners.
About your Halo 4 theory, Bungie has confirmed that there will be no Halo 4. They have confirmed that there will be another game set in the Halo universe, however.