Leilani, now 14, has sat out the Pledge of Allegiance since the second grade.
"Most of my teachers, they respected my decision and my right and belief. So they never said anything about it," she told CNN during a phone interview Friday. "I think the pledge is a lie to me and it's a lie to my people."
Leilani and her family are part of the Elem Indian Colony -- a Native American tribe in Northern California, where she attends Lower Lake High School as a freshman.
During the first week of September, Leilani sat during the flag salute, as she normally does. But this time, her homeroom teacher would not have it. She told Leilani and another Native American student who was also sitting, that they were "making bad choices."
"She told us that we didn't have a choice not to stand up for the pledge," Leilani said. "We told her we have the right to do so. And then she told us that we only have child's rights."
"I was dumbfounded," Leilani said. "She pretty much told us that she could control us. She was forcing everyone in the class to stand up."
A few days later, Leilani recalled, the teacher met with her privately.
"She decided to lower my grade for my lack of participation, supposedly for not standing up for the pledge," said Leilani.
Konocti Unified School District Superintendent Donna Becnel, confirmed Thomas's participation grade was lowered from a 5 to a 3. The other student's grade was also lowered. But Becnel explained that it was a student's right to sit during the Pledge of Allegiance.
"The issue is that she suffered a consequence because she didn't stand," Becnel told CNN. "That is the part about free speech that was not supposed to happen. It is a violation of the student's free speech right to require any student to stand as long as it is not disrupting the learning environment."
Becnel did not identify the teacher involved in the incident, citing confidentiality clauses. CNN requested to interview the teacher for this story but did not receive a response.
"Any consequence or issue with the teacher (is) considered a personnel matter and (is) confidential," Becnel said.
Leilani recorded her exchange with the teacher and shared it with CNN. The conversation appears to start before the recording and go on after the recording ends. Parts of the audio were unintelligible. Becnel said she could not authenticate the recording but that she would not contest it.
During the audio clip, the teacher is heard saying, "Your participation was low because you are sitting."
The teacher goes on, "If you really, really have an argument and feel so strongly about that, then I need to see it written out — your argument — in an essay form. Why? Why, because here's the real thing: those people, they're not alive anymore. Your ancestors, my ancestors. They did a lot of things, I'm not going to argue with you. This is about us now and our future. Trying to be the best we can be, that is really what it's about. It's not about ... you know what I mean? But if you can make a good argument (unintelligible) we'll fix this. I really need a good argument."
Leilani tells the teacher, "I mean, why? There is really no point in putting it into words."
The teacher responds, "It is, because then I know, you've done your research. And then I know that you actually know. (unintelligible) I need you to look at that. The Constitution is not a (unintelligible) document, we are striving to do that. Because what we did before is wrong. "
When Leilani's father, Gary Thomas, heard the recording he was outraged.
"I blew up, to be perfectly honest," Thomas told CNN. "They think that we are extinct. That we are dinosaurs. They think that we are not here, that we don't exist. She should be a lot more sensitive about the district and the place she is teaching in, the children that she is teaching."
Thomas said Leilani has grown up with a deep awareness of Native American history in the United States, even its most violent and bloody chapters.
"I am very knowledgeable of our local history, through the Spanish occupation, when we got the name of the state and when we were traded to America like goods," he said, "So to stand for a flag that has treated my people in that manner, that is a lot more disrespectful than standing for that view."
Thomas was to join the North Dakota's Standing Rock Sioux Tribe in their fight against the Dakota Access Pipeline when Leilani told him about the situation with the pledge and her grades. He decided to stay and stand by his daughter instead.
But even 1,500 miles away from North Dakota, Leilani says she will find a way to make her voice heard in support of Standing Rock.
"As they say 'justice for all'-- we think that is a lie. What they did to my people not long ago? And not so long ago. They still do it today for example with Standing Rock in North Dakota. I want people to realize what has happened and is still happening to the native people to this day. I have my rights to do so," she said.
Both students involved in the incident were moved to other classrooms, where a new teacher will be responsible for their grades, Becnel said.
Asked how she would describe Leilani, Becnel said she is anything but average.
"She is confident, she is articulate, she is well-spoken, she plays in the band," Becnel said. "She is definitely not a trouble-maker."
Leilani, whose Native American name means heavenly flower, says she plans to continue to sit during the Pledge of Allegiance. This, she said, is her stand.
"Someone is standing up, or in this case sitting down, for people who have done a lot of things in the past or the present," she said. "I just hope that she (her teacher) understands why I'm doing it. I don't need to write an essay for her."