The group of General Enriquez was supposedly heading to the town of Baliuag but decided to stay instead in San Rafael, believing it to be a strategic site.

Unknowingly, a Spanish troop from Manila heading towards San Rafael, prepared to silence the 20,000 Filipino insurgents.

Sometime in the middle of the battle, some of the Filipino troops including Colonel Enriquez were separated from the rest of the group and headed to the town of Bigaa (now Balagtas).

Crispin was punished by the sacristan mayor and the town curate, Padre Salvi, and was believed to have died inside the church premises.

In the novel, Rizal told that Rafael's body was formerly buried in the San Diego cemetery before it was exhumed and thrown to the river.

[5][6] The San Juan de Dios Church is a classic example of Partido Baroque architecture in the Philippines.

The style, popular from the early to mid-19th century, boasts of a curved façade as opposed to the flat ones typically found in other Baroque churches in the country.

The church façade has two openings: a main portal now partially covered with a concrete portico and a semi-circular arch window in the center of the second level which provides light to the choir loft.

Located between the convent and the church is a small room containing a painting in memory of the characters Basilio and Crispin from Jose Rizal's Noli Me Tangere.

In the next room, called Museo ng Simbahan (Museum of the Church) are collections of religious items including old stampitas and record books of the parish, a scaled replica of the church retablo, old santos, heavily embroidered vestments and an old episcopal chair.