They start off as enemies and Bellamy even tortures Lincoln at one point for information on the Grounders. Because of Lincoln's romantic relationship with Bellamy's sister, Octavia, Bellamy grows to accept Lincoln as an ally and even saves Lincoln's life after he turns into a Reaper.
Bellamy and Lincoln first meet in Season One'sHis Sister's Keeper when Lincoln stabs Finn. Bellamy captures Lincoln and brings him back to his camp and tortures him in Contents Under Pressure for more information on the Grounders. Bellamy also suspects that Lincoln has taken a liking to Octavia after seeing sketches of her in his journal. In Unity Day, Bellamy discovers the extent of Octavia's and Lincoln's relationship when he sees them embracing and then when Lincoln saves her life. Eventually in We Are Grounders (Part 2), Bellamy sees Lincoln as an ally and allows him to take Octavia to safety in order to save her from her arrow wound.
In the second season, Bellamy commiserates with Octavia when she tells him how she lost Lincoln. Bellamy then helps Octavia capture a Reaper Lincoln in Fog of War and they bring him back to the drop ship so Clarke Griffin can try saving Lincoln (Long Into an Abyss). Later, in Survival of the Fittest, Lincoln agrees to take Bellamy to infiltrate Mount Weather. But, Lincoln is unsure of his ability to resist the Reaper drug. The two men make it to Mount Weather but their plan fails when Lincoln is unable to resist the Reaper drug, which leads to Bellamy's capture. Lincoln finds out from Octavia in Rubicon that in spite of him deserting her brother, Bellamy still successfully made it into Mount Weather.
In His Sister's Keeper, Lincoln had saved Bellamy's sister, Octavia, after she injured herself from falling down a hill. Bellamy goes in search of Octavia, crossing over to Grounder territory where he thinks she might be. His group is attacked and several Delinquents are killed. Octavia witnesses the death of one of them, Roma, because Lincoln saved her from a similar fate. Octavia realizes that if Roma is there, then Bellamy must be looking for her. She asks Lincoln to help him. Lincoln returns her to his cave and chains her up before going back out and blowing his Acid Fog horn to save Bellamy and the others. Bellamy sees Lincoln heading back to his cave and follows after him. When Bellamy enters the cave, he finds an unconscious Lincoln and Octavia, who is trying to free herself from the chains. Bellamy wants to kill Lincoln but Octavia pleads with him not to. Lincoln stabs Finn Collins and almost kills Bellamy before Jasper Jordan knocks him out.
In Contents Under Pressure, With the help of Miller and Drew, Bellamy brings a captured and restrained Lincoln into the drop ship. They tie Lincoln up on the third floor of the drop ship and Bellamy makes Octavia leave when she protests the treatment of him. Bellamy beats Lincoln, trying to get information about the other Grounders, however, Lincoln refuses to speak. Lincoln's belongings are looked through and a collection of vials and a journal are found. In the journal, Bellamy sees a drawing of Octavia and is not pleased. He then sees a drawing of the drop ship and tally marks representing the number of delinquents with ten crossed out for the ten deaths that had already occurred. Clarke soon realizes that the blade Lincoln had stabbed Finn Collins with was poisoned and she and Bellamy escalate the torture as they try to get Lincoln to reveal the antidote. Octavia begs Bellamy to stop, telling him Lincoln had saved their lives even though Finn was dying downstairs. Bellamy continues to brutally torture Lincoln, whipping him with a seatbelt and putting a spike through his hand, yet Lincoln still will not speak. Raven Reyes comes into the room after Finn almost dies again and begins to electrocute the Grounder. Octavia intervenes and slices open her own forearm with the poisoned blade, saying that Lincoln wouldn't let her die. Lincoln helps Octavia find the correct antidote to save her (and Finn).
In Day Trip, Bellamy is unsure what to do with Lincoln but has decided against killing him. Bellamy still won't let Octavia see Lincoln and leaves Miller in charge while he goes on a scavenging mission with Clarke. While he's gone, Octavia helps Lincoln escape.
In Unity Day, Bellamy finds out that it was his sister who helped Lincoln get away and sees them hugging each other. He is less than happy to see the relationship they have but also witnesses Lincoln taking an arrow for Octavia.
In I Am Become Death, Bellamy catches Octavia reading Lincoln's journal. He lets Clarke quarantine her from the hemorrhagic fever that is sweeping through camp, not knowing that Clarke has actually asked Octavia to go talk to Lincoln about the sickness. When Octavia returns, she tells everyone that Lincoln said the sickness is used to weaken them and the Grounders are planning to attack at dawn.
In We Are Grounders (Part 2), During the final battle between the Grounders and the Delinquents, Octavia injures her leg and Bellamy is unable to get her back to the drop ship. Lincoln appears and Bellamy tells Octavia to go with Lincoln because Lincoln can save her and he needs her to live.
In Human Trials, Bellamy comforts Octavia when she tells him about how she wasn't able to save Lincoln from the Reapers.
In Fog of War, Bellamy and Octavia witness Lincoln feasting on the body of Sgt. Scott. Lincoln attacks Octavia and the two fight him off with Octavia eventually shooting Lincoln in the leg. They hide in a car and realize that Lincoln has been turned into a Reaper. Bellamy promises Octavia that they'll get Lincoln back and they come up with a plan to use Octavia as bait. It works and Bellamy is able to knock Lincoln out with an Ark Guard's shock baton. Bellamy tells Octavia that they're taking Lincoln home.
In Long Into an Abyss, Bellamy gets Clarke Griffin from Camp Jaha to go with him back to the drop ship where he and Octavia have chained Lincoln up. Lincoln breaks free and starts attacking them, leading Octavia to knock him out again. They chain him back up and Octavia tries to give Lincoln some water but he gets violent toward her, upsetting her. Bellamy tries to comfort Octavia but she tells him that he can't protect her from this. Later, when Octavia believes Lincoln is dead, Bellamy tries to comfort her.
In Survival of the Fittest, Bellamy and Lincoln are disguised as Reapers as they head toward the Mount Weather mines. Lincoln spears an animal and cuts it open. He smears blood on his face along with limestone to enhance his Reaper disguise. Lincoln tells Bellamy about the intake process and how each person is tagged for either Cerberus Project (like Lincoln) or for Harvest. Bellamy mentions that his mom read mythology to him and Octavia all the time and that Octavia loved it, causing Lincoln to smile. Bellamy asks why he protected Octavia before he knew her. Lincoln then tells Bellamy how when he was a boy, a Sky Person dropped from The Ark and onto Earth. For three days, Lincoln tended to the man, eventually telling his father. His father made Lincoln kill the man and the world has been trying to turn him into a monster for as long as he can remember. Later, Lincoln tells Bellamy that he remembers everything from when he was on the Reaper Red drug.
When they reach the entrance to the Reaper mines, Lincoln appears hesitant, but goes on anyway. As Lincoln and Bellamy make their way through the Reaper tunnels, Lincoln finds himself struggling with his addiction to the Reaper drug. The two discuss the plan to infiltrate and Lincoln again says he doesn't think he can do it. He tries to back out of the plan but they're interrupted by another Reaper Raiding Party and Lincoln has to pretend that Bellamy is his captive to keep their ploy from being discovered. Once they reach the underground entrance to Mount Weather, Bellamy and the other captured grounders are marked for harvesting. Lincoln is unable to resist the Red drug and allows Bellamy to be harvested by the Mountain Men.
In Rubicon, Octavia finds Lincoln in the process of capturing another Grounder to take back to Mount Weather for more of the drug. Lincoln tells her how he betrayed Bellamy and that Bellamy is now a prisoner because of him. Octavia tells Lincoln that Bellamy is fine and he made it.
In Wanheda (Part 1), Lincoln and Bellamy are training. Bellamy then asks Harper to give Lincoln a guard jacket saying the council wanted him to have it. Lincoln states that since he is Trikru, he can not take it but Bellamy convinces him otherwise and says that Octavia will understand eventually.
In Hakeldama, after the massacre of the Trikru army, Lincoln is furious at Bellamy though Bellamy claims "he did what he had to do."
In Stealing Fire, Bellamy meets with Octavia at the dropship in an attempt to help her save Lincoln from execution. However, she sedates him and chains him up in Lincoln's cave with Indra. He tells Octavia he can help her save Lincoln, Kane, and Sinclair but she angrily says that "[He's] the reason they need saving." before leaving him.
In Fallen, the resistance returns to Lincoln's Cave and Bellamy asks where Lincoln is. Octavia beats him mercilessly after saying that Pike put a bullet in his brain.
Bellamy: "Hey, I need to ask you something. You protected my sister before you even knew her. Why? "
Lincoln: "When I was a boy, I saw a ship fall from the sky like Raven's. The man inside was hurt, his body broken. I couldn't get him out."
Bellamy: "Suicide by Earth. I heard the stories in the guard. I just didn't know they were true."
Lincoln: "I brought him food, water. I didn't speak the enemy's language yet so I couldn't understand him but I wanted to. So, on the third day, I told my father. He made me kill him. The world has been trying to turn me into a monster for as long as I can remember. Let's keep moving."