CTF in Arms of Telos is like 2-flag CTF in other games, but has some extra mechanics in play -- as the match progresses and your team captures flags, you advance further into the enemy base until you reach the final flag which will win the game.
It's sort of like this: 3--2--1--||--1--2--3. Starts with both teams at stage 1 flag (Primary Firewall), when you deplete the enemy team’s stage 1 by capping flags, you advance to enemy's stage 2 flag (Backup Firewall), you deplete stage 2 (again by capping flags) to unlock the enemy's stage 3 flag -- unlike the first two stages, stage 3 is one final cap and it wins the game. Also unlike the first two stages, the final flag takes time to deposit.
Your team is always colored blue -- enemy is always orange.
Flag Soaking (Stages 1 and 2 only)
(if you have a better name for this, let me know!)
After you've taken the flag (stage 1 and 2 only), you can stay near the enemy flag stand to soak up more points so that the flag you're holding is worth more. This lets you potentially break through a flag stage in one cap rather than 3.
The Final Flag
Unlike the flags of the first two stages, the final flag holds all of the points for stage 3 and there is no flag soaking. Also unlike the first two stages, simply touching your flag stand with the flag doesn't capture the stage 3 flag entirely.
The player carrying the enemy's final flag must stay near their own flag stand to deposit the points while their teammates defend them. When all the points have been deposited from the enemy's flag, the match ends and you win. Your flag must be present at the flag stand to deposit points from the enemy flag. If you drop the enemy's final flag in range of your flag stand, it will still deposit points, but at a reduced rate.