Solution

• Conrad Wildingham is the killer.
• First: there is evidence that rules out Emma as the killer, although both remaining suspects appear to have very strong motives. Throughout the course of the expedition, Emma is shown to be increasingly passionate about protecting the ghost lynx, as seen through documents such as her field journal pages, textbook page, and others. She viewed Toby as a threat to the ghost lynx's protection - she found out he had plans to publish photos from the expedition early to a magazine called International Terrain, which is referenced in Toby's notebook page from Episode 3. This issue caused her to violently lash out at him and cause him physical harm, which Nigel recounted in the incident report.
• She was also speaking in code with Rusty, which can be seen in several documents. The messages on the luggage tag and bookmark both involve her asking Rusty to take Toby on a hide - more importantly, away from camp. In Toby's notebook page from this episode, he says he returned from one of the hikes to see Emma coming out of the tent he shares with Rusty. She didn't steal anything, but his belongings were moved around. In Toby's notebook page from Episode 1, Toby had written down his laptop ID and password as a reminder to himself. While Emma was inside his tent, she saw his login information and used it on the night he died.
• This fact is supported by two pieces of evidence: one, the bookmark, in which Emma said she was staying in camp for the night. It's not clear on what day this note was written, but Emma asked Rusty if he was resetting a trap after dinner. On the night Toby died, Rusty was indeed resetting a trap after dinner, so it is likely this note was written on the same night. The second piece of evidence is the email chain in this episode. In these emails, we see Toby's interaction with the magazine International Terrain, in which he stated that he intended to share his photos from the expedition. On August 29, the date Toby died, he sent a strange response to the magazine. While he had been eager to work with them before, his tone of writing suddenly changed and he refused to work with the magazine, calling their actions "disgraceful" to the planet. The email was sent at 10:12 PM, which is around the time Toby died, so he couldn't have written the email. This language in the email is reminiscent of Emma's passionate writing in her field journal pages.
• In her field journal page from this episode, she references a "plan" to "deal with" Toby and get him out of camp. At first, this might seem like a plan to murder, but her plan actually involved accessing Toby's laptop in his tent and impersonating him by sending that email. It is clear she wanted to ruin his chance with the magazine, so that nothing about the ghost lynx was published before she could figure out how to properly protect it. If she was in camp sending this email during the time of the murder, then all the suspects' whereabouts are accounted for except for Conrad.
• Conrad's alibi in his field interview was that he was in camp inside his tent doing various activities before bed on the night Toby died. He shares a tent with Nigel, but Nigel was in one of the lab tents writing a weekly report that night. Nigel mentioned in his own field interview that he heard a tent rustling and assumed it must be Conrad, but we now know that Emma was also in camp and inside Toby's tent, so the rustling could have been her. This means that Conrad had the opportunity to commit the murder.
• Conrad's purpose for leading the expedition is to protect his career and reputation by manipulating the expedition results. It is hinted at that Conrad didn't put this expedition together himself - there are several references to Whitlock's President Young arranging the expedition and its funding, such as in the department newsletter and Conrad's video clip. Although he was once confident in his theories, as seen in the Whitlock article from 1992, he did have his doubts if the ghost lynx was even real; Conrad's coded message in Nigel's code notes expresses that doubt. He declares his expedition his last and plans to retire with a nice desk job at the university afterward - this is referenced in the weekly report from Episode 2 and Toby's notebook page from Episode 3.
• There are strong clues that Conrad went into the expedition with a plan to manipulate the outcome. He handpicked all the team members, except for Toby, who got on the project due to his advisor (revealed in Toby's video clip). In the email chain from Episode 5, Conrad expresses that he thinks Emma is incompetent, so why would he choose her for the team? Each team member was focused on their own separate agenda, which would make the expedition and its outcome easier to manipulate. He also brought a contingency to help the team members lose focus - the flask of alcohol (engraved with his initials on the bottom). All of these facts are confirmed in his pocket journal as well.
• On the receipt, he made a note to enact a "plan" either on or by August 31. Later, he scratched out the date and wrote "Catacombs". His plan had to be moved up because he received some bad news - if the expedition came back with nothing conclusive, they would all lose their jobs. Nigel learned this from a university employee in the email chain from Episode 3 and told Conrad. Conrad's plan involved faking evidence of the ghost lynx, which can be inferred from the presence of the feline bone. When compared to the Canada lynx skull in the animal identification chart on DeviantTracker, the feline bone doesn't have the same measurements or characteristics, such as the long sharp canines. This should indicate that the jawbone doesn't belong to a Canada lynx or even a ghost lynx, if it did exist.
• In his pocket journal, Conrad reveals that he brought the bone on the expedition as fake evidence of the ghost lynx. Learning that he might lose his job made him panic and enact the plan earlier. Then Toby discovered Conrad and took photos of him planting the bones in the Catacombs. These photos are revealed through interaction with the DeviantTracker editor.
• Toby wasn't sure what he saw, but Conrad believed Toby would expose him as a fraud and ruin his life. Conrad's motive was to protect his career and reputation. In his pocket journal, Conrad revealed all of this and resolved to get Toby alone. He said he left Toby a note - this note was found in Toby's wallet. The note told Toby that there is something "IT cover worthy" at Echo Cavern at twilight. Toby was murdered outside Echo Cavern sometime between 9:00 PM and 10:15 PM, which is when twilight occurs in Moon Summit during that time of year. The note in Toby's wallet and the tactical knife given to every expedition member were Conrad's means of murder.
• In Michelle's final email response, Conrad confesses to the murder and outlines exactly how the murder was committed.
• Based on all of this information, Conrad Wildingham is the killer.