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When Unicron wakes up there's literally a volcano spewing dark energon everywhere and the humans don't notice? I think not. What was MECH doing during all of this?
In this AU, they find some dark energon from somewhere and take it, thinking that they can use it in their experiments. They find out that it can be used to power machinery and they do so. When they build Nemesis Prime and regular power sources don't work to activate its t-cog, they end up using dark energon, and that works.
Nemesis Prime the episode goes just as it did in canon with Silas going squish and the government taking in the fake Optimus in storage. But the dark energon running in its systems wakes him up and animates him, kind of like Ratchet's tool from way back in Darkness Rising.
But Nemesis is sentient. He can think for himself, move for himself, and he speaks with a distorted version of Optimus' voice because Silas had that installed. Nemesis remembers everything from when the dark energon was first put into him, so he remembers MECH and Silas and experiments and being used. Nemesis didn't like that very much so he walks out of storage and looks for Optimus, because the little he remembers of Optimus makes him the nicest person Nemesis has met in his very short life.
The Autobots find him sooner or later, maybe because Fowler tells them that someone 'stole' Nemesis, and much to their shock, Nemesis is sentient and has no idea what his purpose in life is. The bots are understandably wary of Nemesis at first but Optimus is all 'freedom is the right of all sentient beings' and Nemesis sort of joins them and becomes an Autobot to learn more about Cybertronians because he fits in more with them than with humans despite his creation for obvious reasons.
Miko is the one who gives Nemesis his name despite the fact that it's also the name of the Decepticons' ship. It'll probably cause some confusion down the line. Nemesis also doesn't require energon because he's not alive, he's just a sentient robot. That thought kind of makes him feel really existential because he's literally only a few days to weeks old.
Arcee ends up being all motherly to him once she realizes that he's not that bad because she's the team mom and Optimus is the team dad.
Nemesis can also sort of fix himself with dark energon. Like it heals him when he gets damaged and if he loses an arm he can control it even though it's not attached to him like the zombie Skyquake. And when the other Nemesis gets filled with dark energon and gets a will of his own and starts heading for Manhattan, Nemesis is the only one who's not affected by the stasis beam on account of not being a real Cybertronian and goes in to stop the ship. But they have a small heart to heart talk from one Nemesis to another, because Nemesis Prime doesn't really want to kill the ship until the ship proves that he doesn't care about lives at all and just wants to serve Megatron.
It would be funny if Nemesis convinces the other Nemesis to be his own person and abandon the Decepticons, but for some strange reason I think that'll derail the plot too much. Plus, Nemesis the ship used to be Trypticon and he was definitely an evil Decepticon who worked for Megatron so...
Maybe when Optimus tries to do the thing where he sacrifices himself at the end of season two to destroy the ground bridge, Nemesis stops him and says that he's going to do it himself. Because one, the team needs Optimus more, and two, Nemesis technically can't die. Optimus slowly accepts his argument and Nemesis is the one who's left in the base when the Decepticons fire at it, but he's fine in the end.
So really, it's just a story about an artificial robot gaining sentience because of robot Satan's blood and joining the Autobots all the while dealing with existential crises because does he have a soul or not and if he somehow can actually die then where does said soul go if he even has one because he's definitely not going to any human afterlife and the AllSpark probably won't accept him because he might not have a spark and he's made of dark energon anyway and does that make him inherently unicronic or evil blah blah blah.