Morality is relative
Rather than imagine 'morality' as a consistent score on a character stat that needs to be obscured with trickery until it is dramatically revealed, work on this character's arc and their POV within the story world. Their actions need to make sense to them.
'Morally grey' only has meaning in a black/white world. If the story is set in a morally grey world every character is 'morally grey' (moral-purity in that context would be at odds to the world).
In a literary story with nuanced character development no characters are black/white. They all fall short of their best-intentions, or succumb to the flaw they refused to face.
Avoid turning a good guy to the dark side cliché, and please avoid the scene where the hero pulls off a mask and – SURPRISE – it was his best friend all along (and coincidentally the only other compelling character in the story)!
In the real world 'morality' is probably innate, based completely on our psychological revulsions and attractions, but this character will need something more concrete that motivates them than just secretly hating on the heroes, meanwhile openly aiding them as the plot requires.
He is an antagonist to the heroes, not the readers. The goal is to let the readers know, so they can enjoy the conflict and anticipate sparks. Surprising the reader with a last-act reveal, squanders any character depth and tension.
So how do you keep the main antagonist as redeemable and morally grey
but keep them from becoming thoroughly evil, horrible, and
Here is the real balance you need to make: get the readers to enjoy the antagonist while they are present, causing conflict for the protagonists – not the same as liking or agreeing with them.
Show us their plan. Show them improvising when things go wrong. Give them stakes, make mistakes. Show wins and losses.
We feel empathy when we're involved, whether we like the person or not. In contrast, it's hard to feel anything about a mystery antagonist.
a space war with 2 antagonists
I'll use 2 antagonists from Star Trek: Deep Space Nine specifically because they happen to be interesting contrasts to each other, probably created to be mirror archetypes: male/female, enemy/ally, hedonist/priest, chaotic/rigid.... Each seems designed to be THE specialized antagonist for a specific main character, but evolve to become personally antagonistic to the other MC as well.
Gul Dukat is a charming Nazi. We hear that he was an evil despot, but in-person he's a delight. Despite being evicted, he party-crashes debonair and flirtatious as ever – a clue to how he stomached being the horrible despot: dirt doesn't stick.
At the start of the story Dukat's career is in ruins, but he seems unflappable, and we enjoy characters that are droll under pressure. Over time we see complicated power games as he schemes to get back on top. We learn his flawed (creepy) affinity for the people he subjugated – story arcs make him complicated, then almost redeemable, but ultimately more horrid.
The show constantly resets his topsy-turvy political career. His goals are always selfish, he backstabs everyone, yet we feel sympathy each time success is snatched away. He starts as a simple counterpart to Cisco, but evolves to have an obsession for Kyra too. Mid-series the power flips and Dukat is back on top through a Faustian bargain….
He's a delicious character. Everyone loves a Dukat episode.
His idealogical mirror is Vedek Winn, a rising religious leader. She's a condescending scold to Kyra. We instantly hate her, yet paradoxically she can't openly be criticized. Her episodes are frustrating because the heroes can't touch her, she's not an enemy. Often they must acquiesce to some part of her agenda to accomplish their own goals.
Where Dukat is the life of every party, Winn sucks all joy from the room. Where Dukat hatches schemes that are thwarted, Winn seemingly does nothing – she waits for her rivals to misstep then swoops in. Everyone hates a Kai Winn episode. Her presence in the show indicates someone we like will fail while she undeservedly walks away with the prize.
Dukat is a scenery-chewing villain who is sometimes heroic and complicated. Winn is presented as an irritating schoolmarm that grows slowly into a major ideological threat – not just for the heroes but for their entire agenda. She rises to ruler of the planet, and threatens to erase all the gains they've made.
Unlike charming Dukat, Winn is un-appealing with a glacial rise to power. Her "flaw" appropriately is her pursuit of religious knowledge, which in the ST universe means gaining access to sci-fi artifacts kept locked away for the safety of the galaxy. Again there a contrast, Dukat knows he's an irredeemable scoundrel. Winn's arc is about believing your own bs. Her hubris is to be holier than everyone else, and ultimately that pursuit leads to mystical corruption. (Also she is regular-corrupt because there is zero nuance in ST religion/politics.)
My opinion is that Dukat is the more obvious trope, but done awfully well in a show that needed a campy villain. He brings life to episodes.
Winn is the less-successful rendition. Her arc is monotone and spread thin. The sympathetic flaws come late. We aren't really clued into how important she will become (other than casting a name actress), the politics are too vague to have any stakes, and the religion is Star Trek technobabble™ that never feels weighty. I've read the original idea was to have her sweet at first then do a twist-reveal, which I think is the melodrama cliché of a 'respected leader' trope. Instead they went with a slower, character-driven arc coupled with pseudo-religious shame-dogma. I think it aims a bit higher than ST could hit.