A Theory:

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Foreword: This is almost entirely powered by West Coast Rachel’s idea but I don’t want her to get any hate. This theory is too good to go unshared though. This is also not intended to hurt anyone!

The L/xa that we saw in the Flame/City of Light merged world appeared to Clarke the way Clarke needed to see her and I have an idea as to why.

Clarke knew immediately that the Flame would protect her (once it was successfully implanted in her head) and so she ventured into the CoL trusting that it would take care of her and it did. Not only did it provide a “veil” that kept her hidden from the chipped!Inhabitants of the Col, it also provided her with a guide. 

Who was that guide you may be asking? We all heard the whispered “Clarke” and saw the Infinity sign in the crosswalk sign and the woman’s hair, but those are not the white rabbits (hello Matrix!) that I am referring to. No, the guide the Flame provided Clarke was L/xa herself. 

L/xa did not appear until Clarke was in mortal danger, not just from the chipped!Inhabitants but from the Flame itself. I wonder why she waited that long to reveal herself? The answer is, because L/xa was the Flame. The Flame is a thinking computer, it calculates probabilities and knew that Clarke was dying, that she needed a reason to fight, and so it provided her with one. 

Just as Clarke was giving up, collapsing on the steps, unable to go on, L/xa drops from the sky like an avenging angel. I’ve seen some criticism of the way the fight scene on the stairs was filmed, a slo-mo entrance, the way the shot is angled to position her as the hero saving her defenseless “damsel-in-distress” lover. I believe it was intentional, and here’s why:

The L/xa we saw in the CoL, was essentially a projection of that the Flame created to protect and guide Clarke. The Flame chose to appear as L/xa because she was familiar to Clarke and therefore Clarke would be more likely to trust and follow her. This also explains why the L/xa we see in the City of Light is so much lighter. She smiles often and easily, she’s very physically affectionate with Clarke. She’s free. 

She was also extremely consistent about one thing, she was always guiding Clarke along in her mission. She kept reminding Clarke that she needed to get to the next step, she needed to find the kill switch, she needed to keep going. She was keeping Clarke focused on her task. She even knew things that the real L/xa would never have known. She called the fence a “firewall”. She knew that the sky becoming turbulent meant that ALIE1 was successfully updating her code. L/xa (and the other Grounders) were not technologically advanced in the slightest.

The L/xa that Clarke saw in the City of Light was how Clarke always wanted to be with L/xa. The two of them together, fighting for the same cause, saving both of their people. This time around they can smile with each other, and kiss and hug and joke (”I told you my spirit would choose wisely”). This time around, instead of L/xa abandoning Clarke to certain death at the Mountain, she bravely fought for Clarke, charged into an enemy horde alone and armed with only two blades for her.

This also factors into the way I view Becca in the CoL. I think the Flame’s presence is fluid. I think that once Clarke stepped into Becca’s lab, the Flame was no longer appearing as L/xa and fighting off the chipped!Inhabitants, I think it was focusing all of it’s energy on Clarke and getting her to flip the kill switch. Just like Flame!Becca told Clarke: she created her Father’s watch, something important to her, which helped to guide her.  Just like the kill switch appeared to Clarke as a lever, something she’s pulled twice before-once at the Dropship and once at the Mountain resulting in the deaths of hundreds of people, now she’ll be pulling it to save thousands of people, the image of L/xa in the City of Light was the image that Clarke needed to see. 

This was what Clarke needed to begin her journey towards true absolution. Her real release from guilt for everything that she’s had to do over the last three seasons to save her people. Being able to pull a lever to save people this time instead of kill them, offers Clarke absolution for the lives lost in Mt. Weather and at the Dropship. Wearing her Season 1 clothing and her father’s watch bring Clarke back to a time when she still felt young and happy and carefree, brings her back to the hope that she thought she’d lost. 

Finally, seeing L/xa in the City of Light, allows Clarke to experience her grief properly for the first time. Allows her to obtain absolution for the guilt she was most definitely carrying, for believing that L/xa’s death was in any way her fault, and gives her the opportunity to express the feelings she’d hidden away the last time she saw L/xa alive. To return the “I love you” L/xa surely gave Clarke in that stammering “That’s why you’re you.” moment. It also allows Clarke to give L/xa the send off she should have received from the beginning, a true warrior’s death, fighting to save her people and the woman she loves. Flame! L/xa didn’t say “I love you” back to Clarke because Clarke already knows L/xa loved her, she didn’t need to hear those words. She did need the knowledge that no matter what happens, no matter where she goes, how old she grows, and even when she finds love again, L/xa will always be with her, that to quote L/xa  herself, “Death is not the end.”.

All of the above goes into the importance of the final scene where we get one more parallel (this season has been chock full of them). The last time Clarke lost a lover, Abby collected what was left of them and tried to give them to Clarke and she refused them. Clarke felt guilty about Finn’s death and was not ready to move on and begin to heal. She needed to hold on to the ideal that “Love is Weakness” to push on with what she had to do to save her people. This time, Abby gives Clarke what’s left of L/xa, the Flame, and Clarke accepts it, because she is ready to begin healing, she has received her absolution. 

This finale was so much deeper then just a “Cl/xa reunion” and I think people were either to caught up in their hate for the ship/a character in the ship or their joy/sadness about seeing their ship reunited/knowing that this will be the last time they see L/xa to notice it. 

I’m updating this because the writers just confirmed that this is what they intended with this tidbit right here, taken from the “Script to Screen”:

The embodiment of the Spirit of the Commanders (plural). L/xa represents the Flame, which represents the Commanders. The Flame chooses what it needs to embody at any given moment. 

Agree with this 99.9% apart from the part where it says that L/xa didn’t say “I love you” because Clarke already knew? Like, pretty sure the “I love you” Clarke said was added in in post production, and that’s why you can’t see her face. We all know that if L/xa was told that, she would tear up at least a little (and I think even Flame!L/xa would too) and she didn’t (she didn’t even react), because I don’t believe it was in the original script, but one of JR’s add ins later on?

So, whilst your commentary is right and good (so, so good), and it still fits with this new information, I think it’s hard to think of that area in the scene as something meant originally by the writers, and not last minute fan pandering.

It’s been pretty much confirmed that the “I love you” was ADR (the sound director posted pictures of ADC and Eliza at the studio and the screen in the background showed the scene when they were in front of the door to Becca’s lab).

I just…didn’t want to unintentionally hurt anyone, and I also like the idea that Clarke needed that moment as a sort of catharsis if that makes sense?

I just want to add - that scene being ADR doesn’t necessarily mean it wasn’t in the script. There are a million and one reasons why a scene might need to be dubbed over, an issue with the sound being number 1. I agree with OP’s interpretation of it. That Clarke heard what she needed to hear from her, and in that moment, that wasn’t an “I love you”. Because Clarke was already trying to move on, and her telling L/xa she loved her was her way of closing the door on what they had, while still needing reassurances that L/xa would always be with her. This was a comfort moment, more than anything, to make Leaving L/xa easier to do. Also, not to add fuel to any fire or anything, but the L/xa in the COL was quite clearly not the same L/xa we knew outside of it. It was the L/xa that Clarke and the flame needed her to be, and so no, I don’t think there would have been a heartfelt reaction from L/xa to Clarke’s words - because that’s not the same L/xa that cried while kissing Clarke.