-( Story related, cannot be missed )-
Methuselah has four phases, each progressing into the immediate with a save between (in case you die).
Phase 1: The only real way to properly hurt Methuselah in this phase is to redirect his roaming laser (where he aims at you, then shoots strafing up or down) back at his head. Once this is done enough to bring his health down by a third, a headland opportunity will appear on a joint on his left arm. Land and overcharge it.
Phase 2: He will repeatedly launch a fist rocket at you. Your goal this round is to overcharge boost into his head repeatedly. Four to five hits (for me, fully upgraded) took him out and allowed me to overcharge his right arm.
Phase 3: A repeat of the previous round, but his head will be coated in holo-crystalline energy, making it impenetrable. Luckily, his weakness has been changed to the exposed chestplate. You will need to commandeer one of the Shepherds that spawn in and use them to hit at the weak spot. If you really want to, or if you're quick enough, you could set up an auto-turret body to strike at it while you eliminate the others that spawn in.
Phase 4: Overcharge Boost is the only means, it seemed like, to injure him, though he will not take kindly to you being so close afterwards. One hit might damage him, but it will completely drain your energy gauge. He enjoys charging up and spreading out purple shots all over the place, so as he is charging, get some distance between you and him and use your shield if necessary, then prepare as he will start coming towards you again.