It's hard to determine how canon Master Chief's interations with the Halo 3 Terminals are. The first time Mendicant Bias ackowledges Chief's presence in Terminal 3.
In Terminal 4, he acknowledges the Covenant's presence.
In Terminal 5 he remarks that background processes are attempting to stop his communication with Chief.
Then, in Terminal 7 he sends Chief a direct message through the Terminal:
You don't know the contortions I had to go through to follow you here, Reclaimer. I know what you're here for. What position do I take? Will I follow one betrayal with another?
You're going to say I'm making a habit of turning on my masters.
But the one that destroyed me long ago, in the upper atmosphere of a world far distant from here, was an implement far cruder than I. My weakness was capacity - unintentional though it was! - to choose the Flood. A mistake my makers would not soon forgive.
But I want something far different from you, Reclaimer.
Atonement.
And so here at the end of my life, I do once again betray a former master. The path ahead is fraught with peril. But I will do all I can to keep it stable - keep you safe. I'm not so foolish to think this will absolve me of my sins. One life hardly balances billions.
But I would have my masters know that I have changed.
And you shall be my example.
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Fragments of Mendicant Bias still exist. When he was captured by the IsoDidact aboard Installation 07, he was dismantled for study as their Ancilla's had never turned on them before. His parts were spread all throughout the Ecumene. However, when the Flood began to gain ground in the war, they came across Mendicant's pieces. They rebuilt him out of all the pieces they could find. As such, there were still pieces of him in the Ecumene still under Forerunner control.
So when he made his final assault to try and prevent the Halo Array from being fired, his fleets were defeated as the Halo Pulse wiped out intelligent life aboard his ships. He himself was taken back to the Ark and reprogrammed to think one thought for the rest of his existence. Atonment. So while he isn't at full capacity, he still can interface with certain systems. Because not all of his fragments were recovered though, some still exist in the Orion Arm. One of those being aboard the Forerunner Keyship Truth brought to the Ark. When Mendicant Bias was reunited with that piece, it seems to free him from his locked processes.