At the end both of the Phantoms died. Remember the boss of Inferno? Remember what he said? He said that they should do what they are supposed to do as the Inferno and that means to kill both the phantoms.
The happy thing is at least Elen had her wish fulfilled before her death and Reiji also kept his promise to Elen. They did not die before their wish or promise got fulfilled. That is the happy ending.
As for Reiji, the killer shot him with a silencer. But wait, why was he standing for prolonged time and did not move or speak a word or at least moved a muscle? Because he was so happy at that moment ( because he kept his promise and dreamt to pass the rest of his life by making Elen happy) that he did not even notice the bullet wound. Then finally just dropped on his right side paralyzed; thinking what happened, who shot him. Likely the shot hit on his right side. Remember Scythe master shot him 3 bullets on his left side and was still alive. He might still be alive now. The motivation? It is for Eren. But it could be also the case that the killer made sure he died. As the anime did not make any more episode, so we are concluding that Reiji is dead.
For Eren, she did not realize anything. Because firstly, the Ulanbator spot that we saw was full of mountains, cloud, birds, insects, animals, wind and many more. The sound of the nature can distract you easily. Secondly, Elen was engaged in thinking. She was truly happy because she regained her memory by seeing the sky of Mongolia and feeling the gentle breeze. Just like Reiji got his memory back by seeing his passport. So she happily looked back at Reiji and saw him unconscious by then, lying in the ground. Thats why we saw that even if Elen smiled ( it was for regaining memory), the smile was not complete. As if it was blocked in the midway and so she got her gloomy sad expression of eyes. Or it may be because, she immediately understood the situation that the Inferno is after them. So she had to accept the fate. What will she do now by trying to survive? Why she would live now when Reiji is dead? She just wanted a peaceful life with Reiji. But as her promise of regaining her memory has been fulfilled, she can now gladly die alongside Reiji. Thats why we saw that last smile on her face.
Then the killer also shot her and the bullet we saw in the green field at the very last moment indicates the assassination of Eren. One can argue, if she died by bullet, then where is the blood? Remember Reiji? We also did not see any blood when he was shot.
At the end of the day, Eren died in her motherland peacefully; knowing her identity and also same goes for Reiji. Yes, the anime got separated from the novel. But come on guys, it is just to make the anime more unexpected yet an interesting FINALE. Afterall noone lives forever. If they had to die oneday, be it in their motherland, fulfilling their wishes. This is one happy satisfying end for the phantoms, isn't it?