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Lily had visited the Longbottoms only once after she had gotten pregnant. Harry had been a year old and she had taken no more rebukes. She was going and she was going to see for herself that the Longbottoms were doing well.
She had long since lost her trust in the Wizarding World (and James Potter), and with the knowledge that Voldemort was after her son she needed to gather as many allies as possible.
The entire visit turned out to be a waste of time within moments, and looking back, she had no idea why she had thought the Longbottoms would support her. The Longbottoms were purebloods, just like her husband and his friends, and purebloods always backed each other (especially when the other option was a muggleborn).
Naturally James knew better than her, naturally when he decided to leave their save home in Potter Hall, protected by half a dozen wards and a fidellius that could not broken and instead moved to Godric's Hallow that had zero protections and one fidellius that would protect them (and the fidellius was either kept by a coward who would sell them out in a heartbeat or someone who was more than fine with killing his so-called best friends in the name of a joke).
But no, James was the pureblood wizard and therefore he was right, and for the same reasons her old friends backed him instead of her.
The Longbottoms had listened to her concerns and had then gently told her she was imagining things and that the wards of an old pureblood home would be more than enough to keep her husband and son safe. When it became clear that none of her concerns were being heard, Lily changed course and instead asked after their son.
Neville was apparently a very cute child, but hadn't shown any signs of magic yet (as far as Lily knew it was unusual for a child that young to show any magic), so they were getting a bit worried about it, though it wasn't a pressing concern yet.
The Longbottoms were called away for a moment, leaving Lily alone with both boys and she gently picked up Neville to take a closer look. He was indeed a very cute baby, he also had zero spells placed on him that could protect him in the case the worst would happen.
Lily placed several wandless spells on him, nothing too severe she wasn't capable of that without attracting detection (nothing like what she had placed on Harry, it wasn't like anyone would check him for them), but enough that it would buy him a few valuable seconds if the worst happened.
After that it was a waiting game. Lily didn't believe Voldemort would be defeated without many casualties. She had made precautions, when Voldemort would attack Godric's Hallow she would have a way out. If he didn't attack and the War would resolve in some other way, she would have to think of another way to break free, but she highly doubted it would come to that.
Voldemort, and the Wizarding World, were predictable like that.
In the end it had all happened so quickly that she still barely made it out (she wouldn't forget Severus' sacrifice, it had given her the seconds she needed to survive and she would treasure them forever). She had left Harry inside Godric's Hallow, it wouldn't do for others to grow suspicious and figure out she wasn't as much of a sacrificial lamb as they had wanted her to be.
Her blood had been boiling when she laid in wait in Privet Drive. She had hidden under a car, her large animagus form too conspicuous to stay out in the open, and she had seen Dumbledore and McGonagall leave her son on the front porch of her sister's house without even knocking on the door.
If she hadn't been there Harry could have died from the cold and no one would have even known he was there until it was far too late to save him.
The moment Dumbledore and McGonagall where gone she appeared from within the shadows and grabbed Harry's basket, disappearing into the night. Petunia didn't know a child had been left in her care and no wizard was likely to check on Harry's continued existence until his Hogwarts letter arrived.
She had more than enough time to worry about that at a later point. For now, she needed to go to her hiding place and stay hidden from the Wizarding World. Shouldn't be too hard.
Lily hadn't kept her subscription to the Prophet, it would make finding her far too easy, but she had kept up with the news in the Wizarding World.
The Trial of the Bellatrix, the Lestrange brothers and Barty Crouch Jnr in particular caught her eye. (She had seen Severus had been let go with the help of Dumbledore and she mourned their friendship. He had sold his soul so she might survive and in the end he wouldn't know it had saved her and Harry).
Apparently the Longbottoms had been as flippant with their safety as Lily had been afraid of, and they had been caught off guard. Tortured into insanity before they had been rescued, and yet, nothing seemed to have happened to their son (though people still mourned his lack of magical incidents).
Lily would have liked to say she was surprised by that development, but she was not. That was why she had placed those protection spells on Neville to begin with, children (and especially when still that young) were fragile and if whatever the Deatheaters had done to his parents had turned them into this, it would have surely killed Neville.
She had told herself she wouldn't meddle in that whole affair. Neville had grandparents who would care for him. Neville had money, family and connections, what could she give him that he didn't already have? And apart from that, she wasn't exactly on the run with a toddler, but it was a hard and restless life, how could she do that to another child.
So no, she had done her duty as mother and witch. Neville was alive and it was no longer her concern.
That was until she learned what Neville's loving family did to him while trying to force his body to perform magic, after that it had become her problem again and she wouldn't fail in protecting this child either.
Kidnapping Neville was a lot easier than Lily could have ever predicted it to be. He was still young enough that he didn't worry too much about a strange nice lady (and she would need to have a stranger-danger talk with him once this was over, it was ridiculous how easy it was to entice him to come with her) and with a smile a sweet and the gentle feeling of her magic brushing over him, he followed her deeper into the woods that surrounded the Longbottom residence. Once they were out of reach of the wards, Lily checked Neville for any tracking spells or anything else that could be used to find him (and there were none, why were there none) before Apparating away to the cottage where she had left Harry.
Neville was ecstatic to meet another child his age and happily began playing together with his new friend. Not once did he ask after his parents or grandparents, not when evening fell and Lily brought the two boys to the bedroom they would share, not when a day became two became a week became a month.
The Prophet didn't speak of the missing child of the Longbottom Aurors, no one did. Nor did it once mention the-boy-who-lived no longer being where he was supposed to be. And it was only years later that a stranger appeared on her front porch, hooded eyes and long inky hair falling in his face and an inquisitive and hopeful look that he had never been able to hide from her, that she knew no one was going to ask any questions ever again.