Not a flashback per se, but we relive the memories of didact, and roughly half the gameplay is made up of these flashbacks, half is John searching for these memories and reacting.
As we saw in Halo: Cryptum, a forerunner can impart his memories onto another. He can even impart part of his own physical being onto another via mutations, so much that the imparted being could even be considered the imparter.
Johns ship "lands" inside the sphere. The inside is a lot like the inside of a Halo ring, but it is complete sphereical. Quite unexpectedly he encounters blue team along with Mendez and Halsey. The portal on onyx led here.
He is reunited with his team, and he starts getting vague memories that he can't completely make sense of. He has been imparted with forerunner geas since his early years, which explains why he always "knew" what buttons to press on the halo constructs, and they are what guide him now.
John is guided through a series of trials/puzzles that will unlock the first terminal. Blue team set forth to unlock the terminal, since there isn't much else to go on.
After unlocking the terminal, John accesses it. From there didact imparts his memories onto him. The player plays through the memories as if they were didact himself. They witness the life of the forerunner through these memories.
Roughly half the gameplay is through master chiefs eyes, and roughly half is through master chief seeing through didacts eyes. While John has to deal with forerunner defenses, the gameplay on the side of didacts memories involves many new, forerunner weapons, a forerunner combat skin, fighting against the former human empire (as the forerunner demolished them and set them back to the stone ages), and eventually the flood with the infected forerunner and human forms.
As John and blue team fight from terminal to terminal, gaining didacts memories, they gradually learn how to use forerunner weaponry and eventually are imparted with a forerunner combat skin. Eventually they come into contact with the flood. Infected humans...infected forerunner...infected spartan-IIIs.
THe flood are in the sphere, but how? They have even infected members of the spartan-III squad (that were stuck in slipspace sleep) from onyx. Blue team wants answers, and they'll only get that through didacts memories.
As didacts memories draw to a close, the halo rings are fired. Didact and the remaining forerunner prepare to go on the great journey (whatever that actually is...). But "The prisoner" unbeknownst to them is there. The prisoner traps the didacts and the remaining forerunner within "the great journey". Didact and the forerunner are helpless, ironically being imprisoned by "the prisoner".
The forerunner cannot physically free themselves, but they still have some limited control of technological systems from their "sleep".
Tens of thousands of years pass and humanity comes to rise. It is revealed that ONI was brought about by forerunner geas. All along ONI was secretly a way for the forerunner to guide and help humanity from the great beyond. John was imparted with a geas from birth. He was "the chosen one" so to speak. This explains the the data pads from Halo: Reach. All the ais speaking are forerunner constructs used by the forerunner (through ONI) to try and guide humanity.
John now has all of didacts memories. He also knows where the prisoner is and thusly, Didact and all the trapped forerunner.
He and blue team, equipped with all the forerunner tech imparted to them, seek out the prisoner and put an end to it.
At the end of the trilogy, the very end, we finally see a forerunner as Blue team free them from their prison. Didact tells them everything; they were trapped in a prison, and the memories he gave to John were given so that they could eventually free the forerunner. And so he has. But of course this was didacts plan all along...
The forerunner, freed from the clutches of the prisoner can now properly go on the great journey. Didacts memories are now part of John, and in a nutshell, didact has passed on the title of didact onto John.
John, Blue team and Halsey are imparted with all the knowledge the forerunner have to offer. They know how to use their technology, and they know what exactly the mantle is. The mantle is now humanities to carry.
The forerunner leave for good. Blue team return home to earth. They carry with them the mantle and everything it entails. Any and all forerunner technology and knowledge is now theirs to pass on to humanity. Following the human-covenant-flood war, the galaxy is in shambles, it's falling apart, broken. However John brings back hope for galaxy. Humanity, by taking up the mantle, with the help of the forerunner knowledge they've inherited, will repair the galaxy and become its protectors, much like the forerunner were before them, but hopefully without the flaws.
And so ends Halo.
This also explains the epilogue to Halo: Reach. Reach was a giant ball of flame when the covenant were done with it...how exactly did it become fully terraformed in 30 years?
Forerunner can virtually create planets. With the forerunner tech humanity inherits they could surely repair Reach. That also explains what the odd looking ship in the back left of that cutscene is. That scene takes place 30 years after Halo 3. By then humanity will have integrated forerunner tech into their own, which explains why the ship looks so...inhuman.
[Edited on 06.19.2011 11:41 PM PDT]