First question ever here. This is not my first language so sorry for any mistake. How could a species become the Universe itself, as in controlling every single particle and permeating every form of energy, every scalar field, to become a single entity, a One in a certain way? This species would need to overcome the expansion of the universe for a start?
The universe can become One, but not without great loss. What you are describing is the subjugation and absorption of ever individual intelligence everywhere. The vast majority of the universe's matter wouldn't care that it is being re-purposed; but for that precious fraction of a fraction of a percentage which is intelligence...
you are describing an Apocalypse.
Which leads to the answer that I would offer here.
The ascension of everything into a single universal mind begins with a grey goo scenario. An advanced technological race, which has already mastered FTL, creates a new species of nanites, microscopic self-replicating robots which can adapt to a variety of tasks and purposes. Those nanites quickly get out of control, consuming their creators and their original home planet to create a massive swarm which is ruled by a singular unified AI.
When one of the creator's FTL ships return to the home world, the AI takes it over and uses it to start colonizing other worlds. Soon it is building a fleet of FTL ships and spreading out exponentially over all that exists.
As for the bigger challenges, such as the expanding universe, information-speed-limits and the uncertainty principle, those are challenges for the universal mind to solve. As its' swarm grows to encompass the vast majority of the mass in the universe, it's collective conscious will need to grow proportionally. Perhaps along the way, it will find solutions to the problems we can only loosely define.
It may never encompass everything, but once it commands more than half of all that is, no other force in the universe can oppose it; so its less than total omnipresence and omni-essence will be an academic distinction at best. In all functional definitions, it will BE the universe.
Isaac Asimov tackled that challenge in his Foundation series. A tool you use frequently becomes part of your body ... think of crutches or glasses or pacemakers. The more instrumented those tools — pacemakers, prosthetic limbs, etc — the more they are extensions of self. But there’s also a speed-of-thought aspect. A being that thinks slowly may have its thoughts encoded in slow-to-respond systems. Now take all that to logical extreme: all matter becoming connected by manipulable forces, where gravity extends over infinite distance. All matter gets organized into the body of a single slow-thinking entity. Entire planet ecologies may be considered individual neurons at that scale.
Modern physics suggests a problem with this... The system will break down (the entity will fragment and/or die) as universal inflation continues, unless the entity is able to control dark energy (whatever that turns out to be) to reverse the Big Bang. But if you account for that in your story, it’s a viable concept.
You’ll also need to assume that the entity has solved the quantum gravity problem and discovered some way to eliminate Heisenberg uncertainty in its manipulation of energy. Without that, the entity will only be the entire macroscopic universe, not subatomic.