Kamina and Ryouma started out as rivals but ended up being bros. Same thing for Sheryll and Kamina.
Setsuna admits that he misjudged Heero and says that he's Gundam too, so I guess that counts.
Rand and Gain are bros. Gainer, Renton (the original, at least: he calls Gainer "big brother") and Garrod are bros too.
Maybe Banjo and Roger.

Lockon, Crow and Duo are pretty close friends. Crow even has a support quote for Duo, of all people. He has one for Lockon too, but Duo's was a surprise.

Kallen and Chirico are good friends.

Kallen, Saji, Louise too. The people who studied in Ashford together seem to be amiable to each other. Kouji makes a comment about this if you fight Lelouch with him.

Zero and Sumeragi.

Getter Team and Simon.

The people of General Company (Watta), Zambot 3, Daitarn 3 and Dai-Guard are pretty good friends too.

Kamille and Setsuna. Kamille acts like a "mentor" to Setsuna on Newtype matters.

Michel doesn't trust Lockon at first, but after the Rook Damon mission, where the three snipers have to disable him first, he starts to trust him.

What happened in Stage 57 was as follows:
- Lelouch enacts his Zero Requiem, which is a plan to "collect" all the hate in the world towards a single person, a common enemy, which is him.
- After you down his Damocles, he'll retreat to where the people are going to be executed, like in the final episode of Code Geass R2.
- Suzaku (dressed as Zero) arrives and stabs Zero, "killing" him.
- Later, Zero wakes up in the treatment room of the Ptolemaios 2. He was cured by those pods there.
- Suzaku tells him that the whole world saw Lelouch die, and a lot of the ZEXIS people tell him that they still need him as leader, but because Lelouch is dead, he'll have to be Zero for the rest of his life.
- JIBUN WOOOOO starts playing, and Lelouch accepts becoming Zero again.

Later someone cooks something, and asks Zero to eat it. But since he's using his mask, he opens that eye port (from where he uses Geass).

What I loved about that scene is how Lelouch accepted his responsibility (he's a leader of ZEXIS, not just the Black Knights), and he still has something left to do. Also, his relationship with "Miss Sumeragi" and how Kallen is relieved now that he came back.